[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-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/10005875/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/10013682/transformed.cor.cli.txt"

nPatients in clinical file=127, in cluster file=126, common to both=105
[1]  75 105
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           22                            83 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           22                            83 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           53                            52 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           53                            52 
[1] "AMP PEAK  3(2Q14.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                           32                            73 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                           32                            73 
[1] "AMP PEAK  4(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           70                            35 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           70                            35 
[1] "AMP PEAK  5(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            59                             46 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            59                             46 
[1] "AMP PEAK  6(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                           39                            66 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                           39                            66 
[1] "AMP PEAK  7(6Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE 
                           22                            83 
  AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE 
                           22                            83 
[1] "AMP PEAK  8(7P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE 
                           71                            34 
  AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE 
                           71                            34 
[1] "AMP PEAK  9(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                           70                            35 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                           70                            35 
[1] "AMP PEAK 10(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                           66                            39 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                           66                            39 
[1] "AMP PEAK 11(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                            42                             63 
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                            42                             63 
[1] "AMP PEAK 12(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                            51                             54 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                            51                             54 
[1] "AMP PEAK 13(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                            82                             23 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                            82                             23 
[1] "AMP PEAK 14(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                           21                            84 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                           21                            84 
[1] "AMP PEAK 15(10P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE 
                             29                              76 
  AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE 
                             29                              76 
[1] "AMP PEAK 16(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          28                           77 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          28                           77 
[1] "AMP PEAK 17(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            58                             47 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            58                             47 
[1] "AMP PEAK 18(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                             42                              63 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                             42                              63 
[1] "AMP PEAK 19(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                            48                             57 
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                            48                             57 
[1] "AMP PEAK 20(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                            37                             68 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                            37                             68 
[1] "AMP PEAK 21(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            36                             69 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            36                             69 
[1] "AMP PEAK 22(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                          38                           67 
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                          38                           67 
[1] "AMP PEAK 23(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                             38                              67 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                             38                              67 
[1] "AMP PEAK 24(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                            30                             75 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                            30                             75 
[1] "AMP PEAK 25(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE 
                            19                             86 
  AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE 
                            19                             86 
[1] "AMP PEAK 26(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                          27                           78 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                          27                           78 
[1] "DEL PEAK  1(1P36.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            35                             70 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            35                             70 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           37                            68 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           37                            68 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         14                          91 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         14                          91 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           34                            71 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           34                            71 
[1] "DEL PEAK  5(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           20                            85 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           20                            85 
[1] "DEL PEAK  6(3P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                           60                            45 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                           60                            45 
[1] "DEL PEAK  7(3P14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           71                            34 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           71                            34 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           70                            35 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           70                            35 
[1] "DEL PEAK  9(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           14                            91 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           14                            91 
[1] "DEL PEAK 10(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             8                             97 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             8                             97 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           58                            47 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           58                            47 
[1] "DEL PEAK 12(4Q21.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE 
                            55                             50 
  DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE 
                            55                             50 
[1] "DEL PEAK 13(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                           58                            47 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                           58                            47 
[1] "DEL PEAK 14(4Q31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE 
                           56                            49 
  DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE 
                           56                            49 
[1] "DEL PEAK 15(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE 
                           60                            45 
  DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE 
                           60                            45 
[1] "DEL PEAK 16(5Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                         60                          45 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                         60                          45 
[1] "DEL PEAK 17(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                           37                            68 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                           37                            68 
[1] "DEL PEAK 18(6Q16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE 
                           29                            76 
  DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE 
                           29                            76 
[1] "DEL PEAK 19(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         29                          76 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         29                          76 
[1] "DEL PEAK 20(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           31                            74 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           31                            74 
[1] "DEL PEAK 21(7Q36.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE 
                           37                            68 
  DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE 
                           37                            68 
[1] "DEL PEAK 22(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                           45                            60 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                           45                            60 
[1] "DEL PEAK 23(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                           80                            25 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                           80                            25 
[1] "DEL PEAK 24(10P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE 
                            26                             79 
  DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE 
                            26                             79 
[1] "DEL PEAK 25(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             21                              84 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             21                              84 
[1] "DEL PEAK 26(10Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE 
                            32                             73 
  DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE 
                            32                             73 
[1] "DEL PEAK 27(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             40                              65 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             40                              65 
[1] "DEL PEAK 28(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            44                             61 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            44                             61 
[1] "DEL PEAK 29(11Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE 
                            43                             62 
  DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE 
                            43                             62 
[1] "DEL PEAK 30(12Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE 
                            24                             81 
  DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE 
                            24                             81 
[1] "DEL PEAK 31(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             44                              61 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             44                              61 
[1] "DEL PEAK 32(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            47                             58 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            47                             58 
[1] "DEL PEAK 33(13Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE 
                            41                             64 
  DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE 
                            41                             64 
[1] "DEL PEAK 34(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE 
                            36                             69 
  DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE 
                            36                             69 
[1] "DEL PEAK 35(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            33                             72 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            33                             72 
[1] "DEL PEAK 36(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            47                             58 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            47                             58 
[1] "DEL PEAK 37(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE 
                            46                             59 
  DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE 
                            46                             59 
[1] "DEL PEAK 38(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE 
                            25                             80 
  DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE 
                            25                             80 
[1] "DEL PEAK 39(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                            56                             49 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                            56                             49 
[1] "DEL PEAK 40(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                            61                             44 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                            61                             44 
[1] "DEL PEAK 41(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            46                             59 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            46                             59 
[1] "DEL PEAK 42(19Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE 
                             28                              77 
  DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE 
                             28                              77 
[1] "DEL PEAK 43(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                            21                             84 
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                            21                             84 
[1] "DEL PEAK 44(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                            63                             42 
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                            63                             42 
[1] "DEL PEAK 45(21Q22.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE 
                             61                              44 
  DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE 
                             61                              44 
[1] "DEL PEAK 46(22Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE 
                            42                             63 
  DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE 
                            42                             63 
[1] "DEL PEAK 47(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                           41                            64 
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                           41                            64 
[1] "DEL PEAK 48(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE 
                           43                            62 
  DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE 
                           43                            62 
[1] "DEL PEAK 49(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE 
                            23                             82 
  DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE 
                            23                             82 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "NUMBERPACKYEARSSMOKED"                 
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 105 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        1012          611           NA          632           80          612 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
           1            8           30           16          518           NA 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
          11            4           34           14         3714           NA 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
        1837         1638           NA           NA         1301          189 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
          96          105           NA           NA          272          107 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
         112          102          593          267          195          124 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
          NA          101          218           NA           NA          935 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
          NA          882           NA           NA          211          265 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
          79           NA           11          225          120           92 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
         501           NA           NA          315            2          318 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
           5            2           10           NA            3            4 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
           2            3            2            3            2           NA 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
           4            2            3            3            3            2 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
           2            3            2            6           36           NA 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
          NA           NA           NA           NA          536           NA 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
         115           NA           NA           NA          447           NA 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
         900           NA         1641           NA           NA          267 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
         426           NA          146 
Variable 1:'AGE':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'NUMBERPACKYEARSSMOKED':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "GENDER"               
[7] "NUMBERPACKYEARSSMOKED" "RACE"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 105 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=42, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, 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 18 26 47  3 
[1] "table(vv)"
vv
T0+T1    T2 T3+T4 
   19    26    50 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 18 26 47  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1    T2 T3+T4 
   19    26    50 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
50 33  8  3 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   50    33    11 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
50 33  8  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   50    33    11 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=32, binary=FALSE, numeric=TRUE
RACE, 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   15  6
  AMP PEAK  1(1P34.2) WILD-TYPE 52 25
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           21                            77 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            6                            25 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-L5-A4OM 
       20.78        17.03         0.46       122.10        42.77         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
       18.35         1.38         7.13         0.36         3.95         3.02 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A9 TCGA-R6-A6DN 
       10.45         0.13         0.07         0.10         0.07         8.02 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
       29.59         6.35        53.95 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85         2.63        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.99         0.53         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        1.12        44.75        60.39        53.85         3.68        41.52 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
        6.21         3.16         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         3.16        30.74         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       16.47        21.37        83.24        10.36         0.07         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
        0.07         0.33         0.10         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.07         0.20         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 
        3.78         7.59         5.06        14.70         7.04         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        7.00         8.78        14.01         5.29         4.80 

  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                         0.07                          0.03 
  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 
                         6.35                          3.78 
[1] "0.1 - 122.1 (6.3)" "0.0 - 83.2 (3.8)" 
[1] "hr=" "1.5"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1P34.2) MUTATED         2        1        0        0         4
  AMP PEAK  1(1P34.2) WILD-TYPE       5        3        4        1        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P34.2) MUTATED           4         2          2          1
  AMP PEAK  1(1P34.2) WILD-TYPE        12         9          6          5
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  1(1P34.2) MUTATED            0        0
  AMP PEAK  1(1P34.2) WILD-TYPE          3        1
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  STAGE I                              2                             5
  STAGE IA                             1                             3
  STAGE IB                             0                             4
  STAGE II                             0                             1
  STAGE IIA                            4                            26
  STAGE IIB                            4                            12
  STAGE III                            2                             9
  STAGE IIIA                           2                             6
  STAGE IIIB                           1                             5
  STAGE IIIC                           0                             3
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK  1(1P34.2) MUTATED       6  5     7
  AMP PEAK  1(1P34.2) WILD-TYPE    13 21    43
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T0+T1                           6                            13
  T2                              5                            21
  T3+T4                           7                            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  1(1P34.2) MUTATED    9  7     2
  AMP PEAK  1(1P34.2) WILD-TYPE 41 26     9
D1V5, multiclass
       clus
vv      AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                              9                            41
  N1                              7                            26
  N2+N3                           2                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK  1(1P34.2) MUTATED   14   0  2
  AMP PEAK  1(1P34.2) WILD-TYPE 61   1 13
D1V6, multiclass
     clus
vv    AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  M0                           14                            61
  M1A                           0                             1
  MX                            2                            13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED    3 19
  AMP PEAK  1(1P34.2) WILD-TYPE 12 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      3   19
  AMP PEAK  1(1P34.2) WILD-TYPE   12   71
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                           3                            12
  MALE                            19                            71
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED    7 14
  AMP PEAK  1(1P34.2) WILD-TYPE 28 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      7   14
  AMP PEAK  1(1P34.2) WILD-TYPE   28   52
       clus
vv      AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  ASIAN                           7                            28
  WHITE                          14                            52
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   33 17
  AMP PEAK  2(1Q21.3) WILD-TYPE 34 14
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           50                            48 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           17                            14 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         0.85         2.63         0.03         0.26         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
       17.03         0.79         0.36         0.46       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.68        42.77         0.30        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
        4.08        18.35         7.17         1.38        30.74         4.90 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43         2.60         0.36         7.40         3.95         3.02 
TCGA-L5-A8NJ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       16.47         0.07        10.45         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6DN 
        0.13         0.07         0.10         0.07         0.20         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BV 
        5.06        14.70        29.59         6.35        53.95         8.78 
TCGA-S8-A6BW TCGA-V5-A7RE 
       14.01         4.80 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A6QS TCGA-IG-A7DP 
       33.27        20.78        20.12         0.99         0.13         1.12 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       60.39        53.85        41.52         6.21         3.16         3.45 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OO 
        4.31         8.94         3.52         3.68         3.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        3.16        29.00         7.13         6.94         8.71        25.12 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       21.37        83.24        10.36         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.13         0.10         0.07         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.10         0.07         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB 
        3.78         7.59         7.04         9.30         7.00         5.29 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        4.440                         4.045 
[1] "0.0 - 122.1 (4.4)" "0.1 - 83.2 (4.0)" 
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED         4        2        3        0        11
  AMP PEAK  2(1Q21.3) WILD-TYPE       3        2        1        1        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q21.3) MUTATED           9         6          5          3
  AMP PEAK  2(1Q21.3) WILD-TYPE         7         5          3          3
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED            1        1
  AMP PEAK  2(1Q21.3) WILD-TYPE          2        0
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                              4                             3
  STAGE IA                             2                             2
  STAGE IB                             3                             1
  STAGE II                             0                             1
  STAGE IIA                           11                            19
  STAGE IIB                            9                             7
  STAGE III                            6                             5
  STAGE IIIA                           5                             3
  STAGE IIIB                           3                             3
  STAGE IIIC                           1                             2
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK  2(1Q21.3) MUTATED      11 13    23
  AMP PEAK  2(1Q21.3) WILD-TYPE     8 13    27
D2V4, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T0+T1                          11                             8
  T2                             13                            13
  T3+T4                          23                            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  2(1Q21.3) MUTATED   22 20     5
  AMP PEAK  2(1Q21.3) WILD-TYPE 28 13     6
D2V5, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                             22                            28
  N1                             20                            13
  N2+N3                           5                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK  2(1Q21.3) MUTATED   37   1  7
  AMP PEAK  2(1Q21.3) WILD-TYPE 38   0  8
D2V6, multiclass
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  M0                           37                            38
  M1A                           1                             0
  MX                            7                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED    6 47
  AMP PEAK  2(1Q21.3) WILD-TYPE  9 43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      6   47
  AMP PEAK  2(1Q21.3) WILD-TYPE    9   43
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                           6                             9
  MALE                            47                            43
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   17 36
  AMP PEAK  2(1Q21.3) WILD-TYPE 18 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     17   36
  AMP PEAK  2(1Q21.3) WILD-TYPE   18   30
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                          17                            18
  WHITE                          36                            30
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(2Q14.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(2Q14.2) MUTATED   20  9
  AMP PEAK  3(2Q14.2) WILD-TYPE 47 22
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                           29                            69 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                            9                            22 
$`AMP PEAK  3(2Q14.2) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-JY-A6FA TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH 
       20.09         2.63        44.75         4.31         8.94        19.50 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y 
        4.08         3.32         1.38         7.43         2.60         0.36 
TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A6 
        0.07         0.10         0.07         0.10         0.13         0.10 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.10         0.20         1.18         3.78         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-S8-A6BW TCGA-V5-A7RE 
       14.70         7.04         6.35        14.01         4.80 

$`AMP PEAK  3(2Q14.2) WILD-TYPE`
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         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.99         0.53        17.03         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        1.12         0.46       122.10        60.39        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       41.52        42.77         6.21         3.16         3.45         0.30 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        3.52         3.68         3.35         8.78         6.41        18.35 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        6.94         8.71        25.12         7.40         3.95         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       16.47        21.37        83.24        10.36        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
        0.07         0.33         0.13         0.07         0.10         0.07 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.07         0.10         0.10         0.07         0.07         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       17.62         5.16         8.02        29.59        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        7.00         8.78         5.29 

  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                        44.75                        122.10 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                         3.78                          5.16 
[1] "0.1 - 44.8 (3.8)"  "0.0 - 122.1 (5.2)"
[1] "hr=" "1.5"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(2Q14.2) MUTATED         1        1        2        1         6
  AMP PEAK  3(2Q14.2) WILD-TYPE       6        3        2        0        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(2Q14.2) MUTATED           5         5          2          1
  AMP PEAK  3(2Q14.2) WILD-TYPE        11         6          6          5
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  3(2Q14.2) MUTATED            1        0
  AMP PEAK  3(2Q14.2) WILD-TYPE          2        1
D3V3, multiclass
            clus
vv           AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  STAGE I                              1                             6
  STAGE IA                             1                             3
  STAGE IB                             2                             2
  STAGE II                             1                             0
  STAGE IIA                            6                            24
  STAGE IIB                            5                            11
  STAGE III                            5                             6
  STAGE IIIA                           2                             6
  STAGE IIIB                           1                             5
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK  3(2Q14.2) MUTATED       4  8    15
  AMP PEAK  3(2Q14.2) WILD-TYPE    15 18    35
D3V4, multiclass
       clus
vv      AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  T0+T1                           4                            15
  T2                              8                            18
  T3+T4                          15                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  3(2Q14.2) MUTATED   14  9     4
  AMP PEAK  3(2Q14.2) WILD-TYPE 36 24     7
D3V5, multiclass
       clus
vv      AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  N0                             14                            36
  N1                              9                            24
  N2+N3                           4                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK  3(2Q14.2) MUTATED   20   0  6
  AMP PEAK  3(2Q14.2) WILD-TYPE 55   1  9
D3V6, multiclass
     clus
vv    AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  M0                           20                            55
  M1A                           0                             1
  MX                            6                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(2Q14.2) MUTATED    3 29
  AMP PEAK  3(2Q14.2) WILD-TYPE 12 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q14.2) MUTATED      3   29
  AMP PEAK  3(2Q14.2) WILD-TYPE   12   61
        clus
vv       AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  FEMALE                           3                            12
  MALE                            29                            61
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, binary
                               cls
clus                             0  1
  AMP PEAK  3(2Q14.2) MUTATED   13 18
  AMP PEAK  3(2Q14.2) WILD-TYPE 22 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q14.2) MUTATED     13   18
  AMP PEAK  3(2Q14.2) WILD-TYPE   22   48
       clus
vv      AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  ASIAN                          13                            22
  WHITE                          18                            48
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3Q26.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(3Q26.2) MUTATED   43 20
  AMP PEAK  4(3Q26.2) WILD-TYPE 24 11
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           63                            35 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           20                            11 
$`AMP PEAK  4(3Q26.2) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        0.03         0.26         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH 
        0.13         0.46        44.75        60.39         3.68        42.77 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON 
        3.45         0.30         4.31         3.52         4.08        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-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K 
        6.94         2.60         7.40        16.47        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.07         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.20         1.18         5.16         8.02         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BW 
        6.35        53.95        14.01 

$`AMP PEAK  4(3Q26.2) WILD-TYPE`
TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-KH-A6WC 
        0.99         1.12       122.10        53.85        41.52         6.21 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        3.16         8.94         3.68         3.35        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
        6.41        30.74         4.90         7.43         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49U 
        0.36         3.95         3.02        21.37        83.24         0.07 
TCGA-LN-A49X TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        0.10        17.62         3.78        14.70         7.04        29.59 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78         5.29         4.80 

  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                        60.39                        122.10 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                         2.63                          7.04 
[1] "0.0 - 60.4 (2.6)"  "0.1 - 122.1 (7.0)"
[1] "hr=" "1.8"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(3Q26.2) MUTATED         2        3        3        1        22
  AMP PEAK  4(3Q26.2) WILD-TYPE       5        1        1        0         8
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(3Q26.2) MUTATED          11        10          6          5
  AMP PEAK  4(3Q26.2) WILD-TYPE         5         1          2          1
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  4(3Q26.2) MUTATED            2        0
  AMP PEAK  4(3Q26.2) WILD-TYPE          1        1
D4V3, multiclass
            clus
vv           AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  STAGE I                              2                             5
  STAGE IA                             3                             1
  STAGE IB                             3                             1
  STAGE II                             1                             0
  STAGE IIA                           22                             8
  STAGE IIB                           11                             5
  STAGE III                           10                             1
  STAGE IIIA                           6                             2
  STAGE IIIB                           5                             1
  STAGE IIIC                           2                             1
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK  4(3Q26.2) MUTATED       8 21    36
  AMP PEAK  4(3Q26.2) WILD-TYPE    11  5    14
D4V4, multiclass
       clus
vv      AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  T0+T1                           8                            11
  T2                             21                             5
  T3+T4                          36                            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  4(3Q26.2) MUTATED   34 23     8
  AMP PEAK  4(3Q26.2) WILD-TYPE 16 10     3
D4V5, multiclass
       clus
vv      AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  N0                             34                            16
  N1                             23                            10
  N2+N3                           8                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK  4(3Q26.2) MUTATED   54   0  8
  AMP PEAK  4(3Q26.2) WILD-TYPE 21   1  7
D4V6, multiclass
     clus
vv    AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  M0                           54                            21
  M1A                           0                             1
  MX                            8                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                             0  1
  AMP PEAK  4(3Q26.2) MUTATED    7 63
  AMP PEAK  4(3Q26.2) WILD-TYPE  8 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      7   63
  AMP PEAK  4(3Q26.2) WILD-TYPE    8   27
        clus
vv       AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  FEMALE                           7                             8
  MALE                            63                            27
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, binary
                               cls
clus                             0  1
  AMP PEAK  4(3Q26.2) MUTATED   32 37
  AMP PEAK  4(3Q26.2) WILD-TYPE  3 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED     32   37
  AMP PEAK  4(3Q26.2) WILD-TYPE    3   29
       clus
vv      AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  ASIAN                          32                             3
  WHITE                          37                            29
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5P15.33) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  5(5P15.33) MUTATED   41 13
  AMP PEAK  5(5P15.33) WILD-TYPE 26 18
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            54                             44 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                            13                             18 
$`AMP PEAK  5(5P15.33) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 
       33.27         2.63        20.12         0.03         0.53         0.79 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43C 
        0.46        44.75        53.85         3.68        42.77         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM 
        0.30         4.31         8.94        19.50         8.78         4.08 
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         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K 
        2.60         0.36         3.95        16.47        10.36         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
        0.33         0.10         0.13         0.07         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6KZ 
        0.10         0.07         0.20         1.18         5.16         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
       14.70        29.59        53.95         7.00        14.01         4.80 

$`AMP PEAK  5(5P15.33) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       20.09         0.85        20.78         0.26         0.99        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FG 
        0.36         0.13         1.12       122.10        60.39        41.52 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ 
        6.21         3.45         3.52         3.68         3.35         6.41 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88T 
       18.35         3.32         1.38        30.74         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L 
       25.12         7.40         3.02        21.37        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-M9-A5M8 
        0.16         0.07         0.10         0.13         0.07        17.62 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        3.78         8.02         7.59         7.04         6.35         9.30 
TCGA-S8-A6BV TCGA-V5-A7RB 
        8.78         5.29 

  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                         53.95                         122.10 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                          3.42                           6.38 
[1] "0.0 - 54.0 (3.4)"  "0.1 - 122.1 (6.4)"
[1] "hr=" "1.2"
D5V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(5P15.33) MUTATED         1        3        4        1        18
  AMP PEAK  5(5P15.33) WILD-TYPE       6        1        0        0        12
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(5P15.33) MUTATED           7         9          3          2
  AMP PEAK  5(5P15.33) WILD-TYPE         9         2          5          4
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK  5(5P15.33) MUTATED            2        1
  AMP PEAK  5(5P15.33) WILD-TYPE          1        0
D5V3, multiclass
            clus
vv           AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  STAGE I                               1                              6
  STAGE IA                              3                              1
  STAGE IB                              4                              0
  STAGE II                              1                              0
  STAGE IIA                            18                             12
  STAGE IIB                             7                              9
  STAGE III                             9                              2
  STAGE IIIA                            3                              5
  STAGE IIIB                            2                              4
  STAGE IIIC                            2                              1
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK  5(5P15.33) MUTATED       7 15    32
  AMP PEAK  5(5P15.33) WILD-TYPE    12 11    18
D5V4, multiclass
       clus
vv      AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  T0+T1                            7                             12
  T2                              15                             11
  T3+T4                           32                             18
[1] 3 2
[1] 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(5P15.33) MUTATED   29 20     5
  AMP PEAK  5(5P15.33) WILD-TYPE 21 13     6
D5V5, multiclass
       clus
vv      AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  N0                              29                             21
  N1                              20                             13
  N2+N3                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK  5(5P15.33) MUTATED   42   1 10
  AMP PEAK  5(5P15.33) WILD-TYPE 33   0  5
D5V6, multiclass
     clus
vv    AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  M0                            42                             33
  M1A                            1                              0
  MX                            10                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                                cls
clus                              0  1
  AMP PEAK  5(5P15.33) MUTATED    8 51
  AMP PEAK  5(5P15.33) WILD-TYPE  7 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED      8   51
  AMP PEAK  5(5P15.33) WILD-TYPE    7   39
        clus
vv       AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  FEMALE                            8                              7
  MALE                             51                             39
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, binary
                                cls
clus                              0  1
  AMP PEAK  5(5P15.33) MUTATED   26 31
  AMP PEAK  5(5P15.33) WILD-TYPE  9 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED     26   31
  AMP PEAK  5(5P15.33) WILD-TYPE    9   35
       clus
vv      AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  ASIAN                           26                              9
  WHITE                           31                             35
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(6P21.1) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(6P21.1) MUTATED   26 11
  AMP PEAK  6(6P21.1) WILD-TYPE 41 20
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                           37                            61 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                           11                            20 
$`AMP PEAK  6(6P21.1) MUTATED`
TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.26         0.46       122.10        44.75        60.39        53.85 
TCGA-L5-A43E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        3.45         4.08        18.35         7.17         1.38        30.74 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        7.13         6.94         2.60         0.36         3.95         3.02 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S 
       21.37        10.36         0.07        10.45         0.33         0.13 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 
        0.10         0.10         0.13         0.07         0.10         0.20 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        8.02         7.59        14.70         7.04        29.59        53.95 
TCGA-S8-A6BV 
        8.78 

$`AMP PEAK  6(6P21.1) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         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 
        0.03         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
        0.13         1.12         3.68        41.52        42.77         6.21 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16         0.30         4.31         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR 
        3.35        19.50         8.78         6.41         3.32         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.43         8.71        25.12         7.40 
TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U 
       16.47        83.24         0.16         0.07         0.10         0.07 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.07         0.07         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.07         1.18        17.62         5.16         3.78 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        5.06         6.35         9.30         7.00        14.01         5.29 
TCGA-V5-A7RE 
        4.80 

  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                         6.94                          3.78 
[1] "0.1 - 122.1 (6.9)" "0.0 - 83.2 (3.8)" 
[1] "hr=" "1.5"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(6P21.1) MUTATED         4        2        1        0        12
  AMP PEAK  6(6P21.1) WILD-TYPE       3        2        3        1        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(6P21.1) MUTATED           5         2          2          2
  AMP PEAK  6(6P21.1) WILD-TYPE        11         9          6          4
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  6(6P21.1) MUTATED            1        0
  AMP PEAK  6(6P21.1) WILD-TYPE          2        1
D6V3, multiclass
            clus
vv           AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  STAGE I                              4                             3
  STAGE IA                             2                             2
  STAGE IB                             1                             3
  STAGE II                             0                             1
  STAGE IIA                           12                            18
  STAGE IIB                            5                            11
  STAGE III                            2                             9
  STAGE IIIA                           2                             6
  STAGE IIIB                           2                             4
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK  6(6P21.1) MUTATED       8 10    15
  AMP PEAK  6(6P21.1) WILD-TYPE    11 16    35
D6V4, multiclass
       clus
vv      AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  T0+T1                           8                            11
  T2                             10                            16
  T3+T4                          15                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  6(6P21.1) MUTATED   20  9     4
  AMP PEAK  6(6P21.1) WILD-TYPE 30 24     7
D6V5, multiclass
       clus
vv      AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  N0                             20                            30
  N1                              9                            24
  N2+N3                           4                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK  6(6P21.1) MUTATED   24   0  7
  AMP PEAK  6(6P21.1) WILD-TYPE 51   1  8
D6V6, multiclass
     clus
vv    AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  M0                           24                            51
  M1A                           0                             1
  MX                            7                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                             0  1
  AMP PEAK  6(6P21.1) MUTATED    7 32
  AMP PEAK  6(6P21.1) WILD-TYPE  8 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P21.1) MUTATED      7   32
  AMP PEAK  6(6P21.1) WILD-TYPE    8   58
        clus
vv       AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  FEMALE                           7                             8
  MALE                            32                            58
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, binary
                               cls
clus                             0  1
  AMP PEAK  6(6P21.1) MUTATED   15 23
  AMP PEAK  6(6P21.1) WILD-TYPE 20 43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P21.1) MUTATED     15   23
  AMP PEAK  6(6P21.1) WILD-TYPE   20   43
       clus
vv      AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  ASIAN                          15                            20
  WHITE                          23                            43
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(6Q23.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(6Q23.3) MUTATED   13  7
  AMP PEAK  7(6Q23.3) WILD-TYPE 54 24
  AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE 
                           20                            78 
  AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE 
                            7                            24 
$`AMP PEAK  7(6Q23.3) MUTATED`
TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A4OG 
        0.26       122.10        60.39        53.85         3.45         3.35 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ 
        7.13         7.43         6.94         3.95         3.02        21.37 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49V TCGA-M9-A5M8 TCGA-R6-A6DN 
       10.36        10.45         0.13         0.10        17.62         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 
       14.70         7.04 

$`AMP PEAK  7(6Q23.3) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         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 
        0.03         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
        0.13         1.12         0.46        44.75         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       42.77         6.21         3.16         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.52         3.68        19.50         8.78         6.41         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        4.90        29.00         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
        7.40        16.47        83.24         0.07         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.33         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU 
        0.07         0.10         0.07         0.20         1.18         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        3.78         7.59         5.06        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78        14.01         5.29         4.80 

  AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE 
                         7.28                          3.68 
[1] "0.1 - 122.1 (7.3)" "0.0 - 83.2 (3.7)" 
[1] "hr=" "1.4"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(6Q23.3) MUTATED         5        0        1        0         7
  AMP PEAK  7(6Q23.3) WILD-TYPE       2        4        3        1        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(6Q23.3) MUTATED           2         1          0          1
  AMP PEAK  7(6Q23.3) WILD-TYPE        14        10          8          5
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  7(6Q23.3) MUTATED            1        0
  AMP PEAK  7(6Q23.3) WILD-TYPE          2        1
D7V3, multiclass
            clus
vv           AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE
  STAGE I                              5                             2
  STAGE IA                             0                             4
  STAGE IB                             1                             3
  STAGE II                             0                             1
  STAGE IIA                            7                            23
  STAGE IIB                            2                            14
  STAGE III                            1                            10
  STAGE IIIA                           0                             8
  STAGE IIIB                           1                             5
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK  7(6Q23.3) MUTATED       5  5     9
  AMP PEAK  7(6Q23.3) WILD-TYPE    14 21    41
D7V4, multiclass
       clus
vv      AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE
  T0+T1                           5                            14
  T2                              5                            21
  T3+T4                           9                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  7(6Q23.3) MUTATED   13  4     2
  AMP PEAK  7(6Q23.3) WILD-TYPE 37 29     9
D7V5, multiclass
       clus
vv      AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE
  N0                             13                            37
  N1                              4                            29
  N2+N3                           2                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK  7(6Q23.3) MUTATED   17   0  2
  AMP PEAK  7(6Q23.3) WILD-TYPE 58   1 13
D7V6, multiclass
     clus
vv    AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE
  M0                           17                            58
  M1A                           0                             1
  MX                            2                            13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                             0  1
  AMP PEAK  7(6Q23.3) MUTATED    4 18
  AMP PEAK  7(6Q23.3) WILD-TYPE 11 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6Q23.3) MUTATED      4   18
  AMP PEAK  7(6Q23.3) WILD-TYPE   11   72
        clus
vv       AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE
  FEMALE                           4                            11
  MALE                            18                            72
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, binary
                               cls
clus                             0  1
  AMP PEAK  7(6Q23.3) MUTATED    6 14
  AMP PEAK  7(6Q23.3) WILD-TYPE 29 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6Q23.3) MUTATED      6   14
  AMP PEAK  7(6Q23.3) WILD-TYPE   29   52
       clus
vv      AMP PEAK  7(6Q23.3) MUTATED AMP PEAK  7(6Q23.3) WILD-TYPE
  ASIAN                           6                            29
  WHITE                          14                            52
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7P22.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(7P22.3) MUTATED   48 19
  AMP PEAK  8(7P22.3) WILD-TYPE 19 12
  AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE 
                           67                            31 
  AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE 
                           19                            12 
$`AMP PEAK  8(7P22.3) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
       33.27        20.09         0.85        20.12         0.03         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       17.03         0.79         0.46       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       53.85         3.68        42.77         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94         3.52         3.68         3.35        19.50 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        4.08        18.35         3.32         1.38         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
        4.90        29.00         7.13         6.94         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
        3.95         3.02        16.47        10.36         0.07         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
        0.33         0.10         0.13         0.07         0.07         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.20         1.18         3.78         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
       14.70         7.04        29.59        53.95         9.30         7.00 
TCGA-S8-A6BW 
       14.01 

$`AMP PEAK  8(7P22.3) WILD-TYPE`
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         2.63         0.26         0.99         0.36         0.13 
TCGA-IG-A7DP TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP 
        1.12        41.52         6.21         8.78         6.41         7.17 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L5-A8NU 
        7.43         8.71        25.12         7.40        21.37        83.24 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A8 
       10.45         0.16         0.10         0.07         0.10         0.07 
TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6XQ TCGA-S8-A6BV TCGA-V5-A7RB 
        0.07        17.62         5.16         6.35         8.78         5.29 
TCGA-V5-A7RE 
        4.80 

  AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE 
                         3.68                          6.21 
[1] "0.0 - 122.1 (3.7)" "0.1 - 83.2 (6.2)" 
[1] "hr=" "1.3"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(7P22.3) MUTATED         6        2        3        1        14
  AMP PEAK  8(7P22.3) WILD-TYPE       1        2        1        0        16
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(7P22.3) MUTATED          13        10          4          3
  AMP PEAK  8(7P22.3) WILD-TYPE         3         1          4          3
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  8(7P22.3) MUTATED            2        1
  AMP PEAK  8(7P22.3) WILD-TYPE          1        0
D8V3, multiclass
            clus
vv           AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE
  STAGE I                              6                             1
  STAGE IA                             2                             2
  STAGE IB                             3                             1
  STAGE II                             1                             0
  STAGE IIA                           14                            16
  STAGE IIB                           13                             3
  STAGE III                           10                             1
  STAGE IIIA                           4                             4
  STAGE IIIB                           3                             3
  STAGE IIIC                           2                             1
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK  8(7P22.3) MUTATED      13 14    35
  AMP PEAK  8(7P22.3) WILD-TYPE     6 12    15
D8V4, multiclass
       clus
vv      AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE
  T0+T1                          13                             6
  T2                             14                            12
  T3+T4                          35                            15
[1] 3 2
[1] 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(7P22.3) MUTATED   30 25     7
  AMP PEAK  8(7P22.3) WILD-TYPE 20  8     4
D8V5, multiclass
       clus
vv      AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE
  N0                             30                            20
  N1                             25                             8
  N2+N3                           7                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK  8(7P22.3) MUTATED   48   1  9
  AMP PEAK  8(7P22.3) WILD-TYPE 27   0  6
D8V6, multiclass
     clus
vv    AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE
  M0                           48                            27
  M1A                           1                             0
  MX                            9                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P22.3) MUTATED   10 61
  AMP PEAK  8(7P22.3) WILD-TYPE  5 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.3) MUTATED     10   61
  AMP PEAK  8(7P22.3) WILD-TYPE    5   29
        clus
vv       AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE
  FEMALE                          10                             5
  MALE                            61                            29
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P22.3) MUTATED   24 45
  AMP PEAK  8(7P22.3) WILD-TYPE 11 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.3) MUTATED     24   45
  AMP PEAK  8(7P22.3) WILD-TYPE   11   21
       clus
vv      AMP PEAK  8(7P22.3) MUTATED AMP PEAK  8(7P22.3) WILD-TYPE
  ASIAN                          24                            11
  WHITE                          45                            21
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(7P11.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  9(7P11.2) MUTATED   46 21
  AMP PEAK  9(7P11.2) WILD-TYPE 21 10
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                           67                            31 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                           21                            10 
$`AMP PEAK  9(7P11.2) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D 
       20.09         0.85        20.12         0.03         0.53        17.03 
TCGA-IG-A5B8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43C TCGA-L5-A43E 
        0.79        44.75        60.39        53.85         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         3.52         3.68         3.35        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        6.41         4.08        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T 
       30.74         4.90        29.00         7.13         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L7-A6VZ 
        2.60         0.36         3.95         3.02        16.47        10.36 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        0.07         0.33         0.10         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU 
        0.07         0.10         0.07         0.20         1.18         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        3.78         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB 
        5.29 

$`AMP PEAK  9(7P11.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 
       33.27        20.78         2.63         0.26         0.99         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
        0.13         1.12         0.46       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OX 
       42.77         6.21         8.94         8.78         7.17         7.43 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       25.12         7.40        21.37        83.24        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-R6-A6XG 
        0.07         0.13         0.10         0.07        17.62        29.59 
TCGA-V5-A7RE 
        4.80 

  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                        60.39                        122.10 
  AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE 
                         3.78                          7.17 
[1] "0.0 - 60.4 (3.8)"  "0.1 - 122.1 (7.2)"
[1] "hr=" "1.5"
D9V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(7P11.2) MUTATED         6        2        3        1        14
  AMP PEAK  9(7P11.2) WILD-TYPE       1        2        1        0        16
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(7P11.2) MUTATED          12         9          5          3
  AMP PEAK  9(7P11.2) WILD-TYPE         4         2          3          3
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK  9(7P11.2) MUTATED            2        1
  AMP PEAK  9(7P11.2) WILD-TYPE          1        0
D9V3, multiclass
            clus
vv           AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  STAGE I                              6                             1
  STAGE IA                             2                             2
  STAGE IB                             3                             1
  STAGE II                             1                             0
  STAGE IIA                           14                            16
  STAGE IIB                           12                             4
  STAGE III                            9                             2
  STAGE IIIA                           5                             3
  STAGE IIIB                           3                             3
  STAGE IIIC                           2                             1
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK  9(7P11.2) MUTATED      14 13    34
  AMP PEAK  9(7P11.2) WILD-TYPE     5 13    16
D9V4, multiclass
       clus
vv      AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  T0+T1                          14                             5
  T2                             13                            13
  T3+T4                          34                            16
[1] 3 2
[1] 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(7P11.2) MUTATED   30 25     6
  AMP PEAK  9(7P11.2) WILD-TYPE 20  8     5
D9V5, multiclass
       clus
vv      AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  N0                             30                            20
  N1                             25                             8
  N2+N3                           6                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK  9(7P11.2) MUTATED   46   1 10
  AMP PEAK  9(7P11.2) WILD-TYPE 29   0  5
D9V6, multiclass
     clus
vv    AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  M0                           46                            29
  M1A                           1                             0
  MX                           10                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                             0  1
  AMP PEAK  9(7P11.2) MUTATED   10 60
  AMP PEAK  9(7P11.2) WILD-TYPE  5 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED     10   60
  AMP PEAK  9(7P11.2) WILD-TYPE    5   30
        clus
vv       AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  FEMALE                          10                             5
  MALE                            60                            30
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, binary
                               cls
clus                             0  1
  AMP PEAK  9(7P11.2) MUTATED   23 45
  AMP PEAK  9(7P11.2) WILD-TYPE 12 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P11.2) MUTATED     23   45
  AMP PEAK  9(7P11.2) WILD-TYPE   12   21
       clus
vv      AMP PEAK  9(7P11.2) MUTATED AMP PEAK  9(7P11.2) WILD-TYPE
  ASIAN                          23                            12
  WHITE                          45                            21
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7Q21.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(7Q21.2) MUTATED   44 18
  AMP PEAK 10(7Q21.2) WILD-TYPE 23 13
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                           62                            36 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                           18                            13 
$`AMP PEAK 10(7Q21.2) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
       20.09         2.63        20.12         0.26         0.53        17.03 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
        0.13        44.75        60.39        53.85         3.68        42.77 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
        3.16         3.45         0.30         3.52         3.35        19.50 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        4.08        18.35         3.32         1.38         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
        4.90        29.00         7.13         6.94         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        3.95         3.02        16.47        10.36         0.07        10.45 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
        0.33         0.10         0.13         0.07         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.07         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         0.10         0.20         1.18         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.59         7.04        29.59         6.35         9.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB 
       14.01         5.29 

$`AMP PEAK 10(7Q21.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
       33.27         0.85        20.78         0.03         0.99         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-KH-A6WC 
        0.36         1.12         0.46       122.10        41.52         6.21 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP 
        4.31         8.94         3.68         8.78         6.41         7.17 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L5-A8NU 
        7.43         8.71        25.12         7.40        21.37        83.24 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-M9-A5M8 
        0.16         0.07         0.07         0.10         0.07        17.62 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-V5-A7RE 
        5.16         5.06        14.70        53.95         8.78         4.80 

  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                        60.39                        122.10 
  AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE 
                        3.485                         6.310 
[1] "0.1 - 60.4 (3.5)"  "0.0 - 122.1 (6.3)"
[1] "hr=" "1.1"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(7Q21.2) MUTATED         5        2        2        1        17
  AMP PEAK 10(7Q21.2) WILD-TYPE       2        2        2        0        13
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(7Q21.2) MUTATED          10         9          4          3
  AMP PEAK 10(7Q21.2) WILD-TYPE         6         2          4          3
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 10(7Q21.2) MUTATED            2        1
  AMP PEAK 10(7Q21.2) WILD-TYPE          1        0
D10V3, multiclass
            clus
vv           AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  STAGE I                              5                             2
  STAGE IA                             2                             2
  STAGE IB                             2                             2
  STAGE II                             1                             0
  STAGE IIA                           17                            13
  STAGE IIB                           10                             6
  STAGE III                            9                             2
  STAGE IIIA                           4                             4
  STAGE IIIB                           3                             3
  STAGE IIIC                           2                             1
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK 10(7Q21.2) MUTATED      12 14    33
  AMP PEAK 10(7Q21.2) WILD-TYPE     7 12    17
D10V4, multiclass
       clus
vv      AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  T0+T1                          12                             7
  T2                             14                            12
  T3+T4                          33                            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK 10(7Q21.2) MUTATED   29 24     6
  AMP PEAK 10(7Q21.2) WILD-TYPE 21  9     5
D10V5, multiclass
       clus
vv      AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  N0                             29                            21
  N1                             24                             9
  N2+N3                           6                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK 10(7Q21.2) MUTATED   47   1  8
  AMP PEAK 10(7Q21.2) WILD-TYPE 28   0  7
D10V6, multiclass
     clus
vv    AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  M0                           47                            28
  M1A                           1                             0
  MX                            8                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                             0  1
  AMP PEAK 10(7Q21.2) MUTATED    8 58
  AMP PEAK 10(7Q21.2) WILD-TYPE  7 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED      8   58
  AMP PEAK 10(7Q21.2) WILD-TYPE    7   32
        clus
vv       AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  FEMALE                           8                             7
  MALE                            58                            32
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, binary
                               cls
clus                             0  1
  AMP PEAK 10(7Q21.2) MUTATED   25 39
  AMP PEAK 10(7Q21.2) WILD-TYPE 10 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q21.2) MUTATED     25   39
  AMP PEAK 10(7Q21.2) WILD-TYPE   10   27
       clus
vv      AMP PEAK 10(7Q21.2) MUTATED AMP PEAK 10(7Q21.2) WILD-TYPE
  ASIAN                          25                            10
  WHITE                          39                            27
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(8P11.23) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(8P11.23) MUTATED   26 14
  AMP PEAK 11(8P11.23) WILD-TYPE 41 17
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                            40                             58 
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                            14                             17 
$`AMP PEAK 11(8P11.23) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D 
       33.27        20.09        20.78         0.03         0.26        17.03 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-L5-A43C 
        0.36         0.46       122.10        53.85         3.68         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        3.45         0.30         3.68         8.78         4.08        18.35 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NQ 
        3.16         4.90         7.13         0.36         3.95        21.37 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       10.36         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.13         0.10         0.10         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BW 
       14.70        53.95         7.00        14.01 

$`AMP PEAK 11(8P11.23) WILD-TYPE`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
        0.85         2.63        20.12         0.99         0.53         0.79 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A6FH 
        0.13         1.12        44.75        60.39        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
        6.21         4.31         8.94         3.52         3.35        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        6.41         3.32         7.17         1.38        30.74        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        3.02        16.47        83.24        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.33         0.10         0.07         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.07         0.07         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         3.78         8.02         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         8.78         5.29         4.80 

  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE 
                         3.815                          4.980 
[1] "0.0 - 122.1 (3.8)" "0.1 - 83.2 (5.0)" 
[1] "hr=" "1.3"
D11V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(8P11.23) MUTATED         2        2        1        1        11
  AMP PEAK 11(8P11.23) WILD-TYPE       5        2        3        0        19
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(8P11.23) MUTATED           7         4          1          3
  AMP PEAK 11(8P11.23) WILD-TYPE         9         7          7          3
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 11(8P11.23) MUTATED            2        1
  AMP PEAK 11(8P11.23) WILD-TYPE          1        0
D11V3, multiclass
            clus
vv           AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  STAGE I                               2                              5
  STAGE IA                              2                              2
  STAGE IB                              1                              3
  STAGE II                              1                              0
  STAGE IIA                            11                             19
  STAGE IIB                             7                              9
  STAGE III                             4                              7
  STAGE IIIA                            1                              7
  STAGE IIIB                            3                              3
  STAGE IIIC                            2                              1
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK 11(8P11.23) MUTATED       9  6    22
  AMP PEAK 11(8P11.23) WILD-TYPE    10 20    28
D11V4, multiclass
       clus
vv      AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  T0+T1                            9                             10
  T2                               6                             20
  T3+T4                           22                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 11(8P11.23) MUTATED   20 12     5
  AMP PEAK 11(8P11.23) WILD-TYPE 30 21     6
D11V5, multiclass
       clus
vv      AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  N0                              20                             30
  N1                              12                             21
  N2+N3                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK 11(8P11.23) MUTATED   28   1  5
  AMP PEAK 11(8P11.23) WILD-TYPE 47   0 10
D11V6, multiclass
     clus
vv    AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  M0                            28                             47
  M1A                            1                              0
  MX                             5                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                                cls
clus                              0  1
  AMP PEAK 11(8P11.23) MUTATED    6 36
  AMP PEAK 11(8P11.23) WILD-TYPE  9 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.23) MUTATED      6   36
  AMP PEAK 11(8P11.23) WILD-TYPE    9   54
        clus
vv       AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  FEMALE                            6                              9
  MALE                             36                             54
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, binary
                                cls
clus                              0  1
  AMP PEAK 11(8P11.23) MUTATED   14 27
  AMP PEAK 11(8P11.23) WILD-TYPE 21 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.23) MUTATED     14   27
  AMP PEAK 11(8P11.23) WILD-TYPE   21   39
       clus
vv      AMP PEAK 11(8P11.23) MUTATED AMP PEAK 11(8P11.23) WILD-TYPE
  ASIAN                           14                             21
  WHITE                           27                             39
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8P11.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(8P11.21) MUTATED   30 17
  AMP PEAK 12(8P11.21) WILD-TYPE 37 14
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                            47                             51 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                            17                             14 
$`AMP PEAK 12(8P11.21) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D 
       33.27        20.09        20.78         0.03         0.26        17.03 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.36         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OI 
        3.68         3.16         3.45         0.30         3.68         8.78 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
        4.08        18.35         3.32         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K 
        7.43         0.36         3.95        21.37        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       10.45         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-R6-A6DQ 
        0.07         0.10         0.10         0.07         0.10         7.59 
TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        5.06        53.95         7.00         8.78        14.01 

$`AMP PEAK 12(8P11.21) WILD-TYPE`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
        0.85         2.63        20.12         0.99         0.53         0.79 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43J 
        0.13         1.12        41.52        42.77         6.21         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP 
        8.94         3.52         3.35        19.50         6.41         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        1.38        30.74        29.00         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49M 
       25.12         7.40         3.02        16.47        83.24         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A5 
        0.07         0.33         0.10         0.07         0.13         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.07         0.20         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        3.78         8.02        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         5.29         4.80 

  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                          3.95                           4.80 
[1] "0.0 - 122.1 (4.0)" "0.1 - 83.2 (4.8)" 
[1] "hr=" "1.2"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(8P11.21) MUTATED         3        2        1        1        14
  AMP PEAK 12(8P11.21) WILD-TYPE       4        2        3        0        16
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(8P11.21) MUTATED           9         6          2          3
  AMP PEAK 12(8P11.21) WILD-TYPE         7         5          6          3
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 12(8P11.21) MUTATED            3        1
  AMP PEAK 12(8P11.21) WILD-TYPE          0        0
D12V3, multiclass
            clus
vv           AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  STAGE I                               3                              4
  STAGE IA                              2                              2
  STAGE IB                              1                              3
  STAGE II                              1                              0
  STAGE IIA                            14                             16
  STAGE IIB                             9                              7
  STAGE III                             6                              5
  STAGE IIIA                            2                              6
  STAGE IIIB                            3                              3
  STAGE IIIC                            3                              0
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK 12(8P11.21) MUTATED      10 11    26
  AMP PEAK 12(8P11.21) WILD-TYPE     9 15    24
D12V4, multiclass
       clus
vv      AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  T0+T1                           10                              9
  T2                              11                             15
  T3+T4                           26                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 12(8P11.21) MUTATED   24 17     6
  AMP PEAK 12(8P11.21) WILD-TYPE 26 16     5
D12V5, multiclass
       clus
vv      AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  N0                              24                             26
  N1                              17                             16
  N2+N3                            6                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK 12(8P11.21) MUTATED   37   1  6
  AMP PEAK 12(8P11.21) WILD-TYPE 38   0  9
D12V6, multiclass
     clus
vv    AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  M0                            37                             38
  M1A                            1                              0
  MX                             6                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                                cls
clus                              0  1
  AMP PEAK 12(8P11.21) MUTATED    6 45
  AMP PEAK 12(8P11.21) WILD-TYPE  9 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED      6   45
  AMP PEAK 12(8P11.21) WILD-TYPE    9   45
        clus
vv       AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  FEMALE                            6                              9
  MALE                             45                             45
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, binary
                                cls
clus                              0  1
  AMP PEAK 12(8P11.21) MUTATED   20 30
  AMP PEAK 12(8P11.21) WILD-TYPE 15 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED     20   30
  AMP PEAK 12(8P11.21) WILD-TYPE   15   36
       clus
vv      AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  ASIAN                           20                             15
  WHITE                           30                             36
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8Q24.21) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(8Q24.21) MUTATED   51 24
  AMP PEAK 13(8Q24.21) WILD-TYPE 16  7
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                            75                             23 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                            24                              7 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.53        17.03         0.79         0.36         0.13 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.46       122.10        44.75        60.39        53.85         3.68 
TCGA-JY-A6FG TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       41.52         3.16         3.45         0.30         4.31         3.52 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       19.50         8.78         6.41         4.08        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        30.74         4.90         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K 
        2.60         0.36         3.95        21.37        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.07         0.10         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.07         0.10         0.10         0.10         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.20         1.18         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV 
       14.70         7.04        29.59        53.95         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       14.01         5.29         4.80 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43M 
        0.03         0.99         1.12        42.77         6.21         8.94 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T 
        3.68         3.35         7.17        29.00         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A4A8 
       25.12         7.40         3.02        16.47        83.24         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6XQ TCGA-R6-A6Y2 
       17.62         5.16         3.78         6.35         9.30 

  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          3.52                           6.94 
[1] "0.1 - 122.1 (3.5)" "0.0 - 83.2 (6.9)" 
[1] "hr=" "1.4"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(8Q24.21) MUTATED         5        2        3        1        23
  AMP PEAK 13(8Q24.21) WILD-TYPE       2        2        1        0         7
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(8Q24.21) MUTATED          12        10          7          4
  AMP PEAK 13(8Q24.21) WILD-TYPE         4         1          1          2
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 13(8Q24.21) MUTATED            3        1
  AMP PEAK 13(8Q24.21) WILD-TYPE          0        0
D13V3, multiclass
            clus
vv           AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  STAGE I                               5                              2
  STAGE IA                              2                              2
  STAGE IB                              3                              1
  STAGE II                              1                              0
  STAGE IIA                            23                              7
  STAGE IIB                            12                              4
  STAGE III                            10                              1
  STAGE IIIA                            7                              1
  STAGE IIIB                            4                              2
  STAGE IIIC                            3                              0
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK 13(8Q24.21) MUTATED      13 21    40
  AMP PEAK 13(8Q24.21) WILD-TYPE     6  5    10
D13V4, multiclass
       clus
vv      AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  T0+T1                           13                              6
  T2                              21                              5
  T3+T4                           40                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 13(8Q24.21) MUTATED   39 27     8
  AMP PEAK 13(8Q24.21) WILD-TYPE 11  6     3
D13V5, multiclass
       clus
vv      AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  N0                              39                             11
  N1                              27                              6
  N2+N3                            8                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK 13(8Q24.21) MUTATED   60   1 10
  AMP PEAK 13(8Q24.21) WILD-TYPE 15   0  5
D13V6, multiclass
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  M0                            60                             15
  M1A                            1                              0
  MX                            10                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                                cls
clus                              0  1
  AMP PEAK 13(8Q24.21) MUTATED    8 74
  AMP PEAK 13(8Q24.21) WILD-TYPE  7 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      8   74
  AMP PEAK 13(8Q24.21) WILD-TYPE    7   16
        clus
vv       AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  FEMALE                            8                              7
  MALE                             74                             16
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, binary
                                cls
clus                              0  1
  AMP PEAK 13(8Q24.21) MUTATED   34 46
  AMP PEAK 13(8Q24.21) WILD-TYPE  1 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     34   46
  AMP PEAK 13(8Q24.21) WILD-TYPE    1   20
       clus
vv      AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  ASIAN                           34                              1
  WHITE                           46                             20
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(9P13.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 14(9P13.3) MUTATED   12  6
  AMP PEAK 14(9P13.3) WILD-TYPE 55 25
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                           18                            80 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                            6                            25 
$`AMP PEAK 14(9P13.3) MUTATED`
TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43H TCGA-L5-A43J 
        0.36       122.10        53.85        42.77         0.30         4.31 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L7-A6VZ TCGA-LN-A49K 
       19.50        18.35        29.00         0.36        10.36         0.07 
TCGA-LN-A49O TCGA-LN-A4MQ TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-S8-A6BW 
        0.33         0.10         3.78         5.06        14.70        14.01 

$`AMP PEAK 14(9P13.3) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        0.03         0.26         0.99         0.53        17.03         0.79 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
        0.13         1.12         0.46        44.75        60.39         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE 
       41.52         6.21         3.16         3.45         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
        3.68         3.35         8.78         6.41         4.08         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        7.17         1.38         3.16        30.74         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L 
        3.95         3.02        16.47        21.37        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.16         0.07         0.10         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.10         0.07         0.07         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
        1.18        17.62         5.16         8.02         7.59         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
       29.59         6.35        53.95         9.30         7.00         8.78 
TCGA-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                        7.710                         3.815 
[1] "0.1 - 122.1 (7.7)" "0.0 - 83.2 (3.8)" 
[1] "hr=" "1.4"
D14V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(9P13.3) MUTATED         2        0        1        0         6
  AMP PEAK 14(9P13.3) WILD-TYPE       5        4        3        1        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(9P13.3) MUTATED           3         3          0          2
  AMP PEAK 14(9P13.3) WILD-TYPE        13         8          8          4
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 14(9P13.3) MUTATED            1        0
  AMP PEAK 14(9P13.3) WILD-TYPE          2        1
D14V3, multiclass
            clus
vv           AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  STAGE I                              2                             5
  STAGE IA                             0                             4
  STAGE IB                             1                             3
  STAGE II                             0                             1
  STAGE IIA                            6                            24
  STAGE IIB                            3                            13
  STAGE III                            3                             8
  STAGE IIIA                           0                             8
  STAGE IIIB                           2                             4
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  AMP PEAK 14(9P13.3) MUTATED       4  3    12
  AMP PEAK 14(9P13.3) WILD-TYPE    15 23    38
D14V4, multiclass
       clus
vv      AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  T0+T1                           4                            15
  T2                              3                            23
  T3+T4                          12                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK 14(9P13.3) MUTATED   11  5     3
  AMP PEAK 14(9P13.3) WILD-TYPE 39 28     8
D14V5, multiclass
       clus
vv      AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  N0                             11                            39
  N1                              5                            28
  N2+N3                           3                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  AMP PEAK 14(9P13.3) MUTATED   14   0  4
  AMP PEAK 14(9P13.3) WILD-TYPE 61   1 11
D14V6, multiclass
     clus
vv    AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  M0                           14                            61
  M1A                           0                             1
  MX                            4                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                               cls
clus                             0  1
  AMP PEAK 14(9P13.3) MUTATED    1 20
  AMP PEAK 14(9P13.3) WILD-TYPE 14 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED      1   20
  AMP PEAK 14(9P13.3) WILD-TYPE   14   70
        clus
vv       AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  FEMALE                           1                            14
  MALE                            20                            70
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, binary
                               cls
clus                             0  1
  AMP PEAK 14(9P13.3) MUTATED    8 13
  AMP PEAK 14(9P13.3) WILD-TYPE 27 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED      8   13
  AMP PEAK 14(9P13.3) WILD-TYPE   27   53
       clus
vv      AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  ASIAN                           8                            27
  WHITE                          13                            53
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(10P11.21) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 15(10P11.21) MUTATED   18  7
  AMP PEAK 15(10P11.21) WILD-TYPE 49 24
  AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE 
                             25                              73 
  AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE 
                              7                              24 
$`AMP PEAK 15(10P11.21) MUTATED`
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
        0.46       122.10         3.68         3.16         0.30         3.68 
TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L7-A6VZ 
       19.50         3.16         2.60         3.02        16.47        10.36 
TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A4 
       10.45         0.10         0.13         0.07         0.07         0.10 
TCGA-LN-A4A6 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-S8-A6BW 
        0.10         3.78         8.02         5.06         6.35        14.01 
TCGA-V5-A7RE 
        4.80 

$`AMP PEAK 15(10P11.21) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        0.03         0.26         0.99         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.36         0.13         1.12        44.75        60.39        53.85 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M 
       41.52        42.77         6.21         3.45         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.52         3.35         8.78         6.41         4.08        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        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         7.43         6.94         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M 
        7.40         3.95        21.37        83.24         0.07         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.07         0.33         0.10         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.07         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6L4 
        0.20         1.18        17.62         5.16         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04        29.59        53.95         9.30         7.00         8.78 
TCGA-V5-A7RB 
        5.29 

  AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE 
                           0.07                            0.03 
  AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE 
                         122.10                           83.24 
  AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE 
                           3.68                            5.16 
[1] "0.1 - 122.1 (3.7)" "0.0 - 83.2 (5.2)" 
[1] "hr=" "1.1"
D15V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(10P11.21) MUTATED         3        1        2        1         7
  AMP PEAK 15(10P11.21) WILD-TYPE       4        3        2        0        23
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(10P11.21) MUTATED           1         7          0          2
  AMP PEAK 15(10P11.21) WILD-TYPE        15         4          8          4
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 15(10P11.21) MUTATED            1        0
  AMP PEAK 15(10P11.21) WILD-TYPE          2        1
D15V3, multiclass
            clus
vv           AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE
  STAGE I                                3                               4
  STAGE IA                               1                               3
  STAGE IB                               2                               2
  STAGE II                               1                               0
  STAGE IIA                              7                              23
  STAGE IIB                              1                              15
  STAGE III                              7                               4
  STAGE IIIA                             0                               8
  STAGE IIIB                             2                               4
  STAGE IIIC                             1                               2
  STAGE IV                               0                               1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3+T4
  AMP PEAK 15(10P11.21) MUTATED       6  5    14
  AMP PEAK 15(10P11.21) WILD-TYPE    13 21    36
D15V4, multiclass
       clus
vv      AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE
  T0+T1                             6                              13
  T2                                5                              21
  T3+T4                            14                              36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  AMP PEAK 15(10P11.21) MUTATED   14  8     3
  AMP PEAK 15(10P11.21) WILD-TYPE 36 25     8
D15V5, multiclass
       clus
vv      AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE
  N0                               14                              36
  N1                                8                              25
  N2+N3                             3                               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1A MX
  AMP PEAK 15(10P11.21) MUTATED   20   0  4
  AMP PEAK 15(10P11.21) WILD-TYPE 55   1 11
D15V6, multiclass
     clus
vv    AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE
  M0                             20                              55
  M1A                             0                               1
  MX                              4                              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                 cls
clus                               0  1
  AMP PEAK 15(10P11.21) MUTATED    1 28
  AMP PEAK 15(10P11.21) WILD-TYPE 14 62
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(10P11.21) MUTATED      1   28
  AMP PEAK 15(10P11.21) WILD-TYPE   14   62
        clus
vv       AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE
  FEMALE                             1                              14
  MALE                              28                              62
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, binary
                                 cls
clus                               0  1
  AMP PEAK 15(10P11.21) MUTATED   12 17
  AMP PEAK 15(10P11.21) WILD-TYPE 23 49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(10P11.21) MUTATED     12   17
  AMP PEAK 15(10P11.21) WILD-TYPE   23   49
       clus
vv      AMP PEAK 15(10P11.21) MUTATED AMP PEAK 15(10P11.21) WILD-TYPE
  ASIAN                            12                              23
  WHITE                            17                              49
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(11P13) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 16(11P13) MUTATED   16  8
  AMP PEAK 16(11P13) WILD-TYPE 51 23
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          24                           74 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                           8                           23 
$`AMP PEAK 16(11P13) MUTATED`
TCGA-IG-A50L TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OE 
        0.53       122.10         3.68         6.21         8.94         3.52 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S 
       19.50         4.08        18.35         4.90        29.00         6.94 
TCGA-L5-A891 TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4MQ TCGA-LN-A4MR 
        3.95         0.07         0.13         0.10         0.10         0.07 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO 
        3.78         7.59         7.04         6.35        53.95         7.00 

$`AMP PEAK 16(11P13) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         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-A625 
        0.03         0.26         0.99        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12         0.46        44.75        60.39        53.85 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       41.52        42.77         3.16         3.45         0.30         4.31 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
        3.68         3.35         8.78         6.41         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        1.38         3.16        30.74         7.13         7.43         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NJ 
        2.60        25.12         0.36         7.40         3.02        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        83.24        10.36        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.33         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN 
        0.07         0.20         1.18        17.62         5.16         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW 
        5.06        14.70        29.59         9.30         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                      122.10                        83.24 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                       5.555                        3.565 
[1] "0.1 - 122.1 (5.6)" "0.0 - 83.2 (3.6)" 
[1] "hr=" "1"  
D16V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(11P13) MUTATED         2        2        1        0         8
  AMP PEAK 16(11P13) WILD-TYPE       5        2        3        1        22
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(11P13) MUTATED           2         3          1          2
  AMP PEAK 16(11P13) WILD-TYPE        14         8          7          4
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 16(11P13) MUTATED            0        1
  AMP PEAK 16(11P13) WILD-TYPE          3        0
D16V3, multiclass
            clus
vv           AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  STAGE I                             2                            5
  STAGE IA                            2                            2
  STAGE IB                            1                            3
  STAGE II                            0                            1
  STAGE IIA                           8                           22
  STAGE IIB                           2                           14
  STAGE III                           3                            8
  STAGE IIIA                          1                            7
  STAGE IIIB                          2                            4
  STAGE IIIC                          0                            3
  STAGE IV                            1                            0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3+T4
  AMP PEAK 16(11P13) MUTATED       6  2    16
  AMP PEAK 16(11P13) WILD-TYPE    13 24    34
D16V4, multiclass
       clus
vv      AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  T0+T1                          6                           13
  T2                             2                           24
  T3+T4                         16                           34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2+N3
  AMP PEAK 16(11P13) MUTATED   13  8     3
  AMP PEAK 16(11P13) WILD-TYPE 37 25     8
D16V5, multiclass
       clus
vv      AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  N0                            13                           37
  N1                             8                           25
  N2+N3                          3                            8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1A MX
  AMP PEAK 16(11P13) MUTATED   18   1  2
  AMP PEAK 16(11P13) WILD-TYPE 57   0 13
D16V6, multiclass
     clus
vv    AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  M0                          18                           57
  M1A                          1                            0
  MX                           2                           13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                              cls
clus                            0  1
  AMP PEAK 16(11P13) MUTATED    4 24
  AMP PEAK 16(11P13) WILD-TYPE 11 66
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(11P13) MUTATED      4   24
  AMP PEAK 16(11P13) WILD-TYPE   11   66
        clus
vv       AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  FEMALE                          4                           11
  MALE                           24                           66
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, binary
                              cls
clus                            0  1
  AMP PEAK 16(11P13) MUTATED   10 17
  AMP PEAK 16(11P13) WILD-TYPE 25 49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(11P13) MUTATED     10   17
  AMP PEAK 16(11P13) WILD-TYPE   25   49
       clus
vv      AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  ASIAN                         10                           25
  WHITE                         17                           49
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(11Q13.3) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 17(11Q13.3) MUTATED   40 13
  AMP PEAK 17(11Q13.3) WILD-TYPE 27 18
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            53                             45 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            13                             18 
$`AMP PEAK 17(11Q13.3) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D 
       33.27         0.85        20.78        20.12         0.03        17.03 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43H 
        0.13         0.46       122.10        60.39         3.68         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94         3.52         3.68         3.35        19.50 
TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V 
        4.08         1.38        30.74        29.00         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
        0.36         3.95        21.37         0.07         0.16         0.07 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.10         0.13         0.10         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.10         0.07         0.20         1.18         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO 
        7.59         7.04         6.35        53.95         7.00 

$`AMP PEAK 17(11Q13.3) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.09         2.63         0.26         0.99         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
        0.36         1.12        44.75        53.85        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        6.21         3.16         3.45         8.78         6.41        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         7.17         3.16         4.90         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NU 
        8.71        25.12         7.40         3.02        16.47        83.24 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A4A9 TCGA-M9-A5M8 
       10.36        10.45         0.33         0.07         0.07        17.62 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-S8-A6BV 
        5.16         5.06        14.70        29.59         9.30         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       14.01         5.29         4.80 

  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                          2.60                           7.13 
[1] "0.0 - 122.1 (2.6)" "0.1 - 83.2 (7.1)" 
[1] "hr=" "1.1"
D17V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(11Q13.3) MUTATED         4        1        1        1        18
  AMP PEAK 17(11Q13.3) WILD-TYPE       3        3        3        0        12
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(11Q13.3) MUTATED           9         9          4          3
  AMP PEAK 17(11Q13.3) WILD-TYPE         7         2          4          3
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 17(11Q13.3) MUTATED            0        0
  AMP PEAK 17(11Q13.3) WILD-TYPE          3        1
D17V3, multiclass
            clus
vv           AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  STAGE I                               4                              3
  STAGE IA                              1                              3
  STAGE IB                              1                              3
  STAGE II                              1                              0
  STAGE IIA                            18                             12
  STAGE IIB                             9                              7
  STAGE III                             9                              2
  STAGE IIIA                            4                              4
  STAGE IIIB                            3                              3
  STAGE IIIC                            0                              3
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK 17(11Q13.3) MUTATED       9 16    28
  AMP PEAK 17(11Q13.3) WILD-TYPE    10 10    22
D17V4, multiclass
       clus
vv      AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  T0+T1                            9                             10
  T2                              16                             10
  T3+T4                           28                             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 17(11Q13.3) MUTATED   29 19     5
  AMP PEAK 17(11Q13.3) WILD-TYPE 21 14     6
D17V5, multiclass
       clus
vv      AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  N0                              29                             21
  N1                              19                             14
  N2+N3                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK 17(11Q13.3) MUTATED   44   0  6
  AMP PEAK 17(11Q13.3) WILD-TYPE 31   1  9
D17V6, multiclass
     clus
vv    AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  M0                            44                             31
  M1A                            0                              1
  MX                             6                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                              0  1
  AMP PEAK 17(11Q13.3) MUTATED    7 51
  AMP PEAK 17(11Q13.3) WILD-TYPE  8 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED      7   51
  AMP PEAK 17(11Q13.3) WILD-TYPE    8   39
        clus
vv       AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  FEMALE                            7                              8
  MALE                             51                             39
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, binary
                                cls
clus                              0  1
  AMP PEAK 17(11Q13.3) MUTATED   25 32
  AMP PEAK 17(11Q13.3) WILD-TYPE 10 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     25   32
  AMP PEAK 17(11Q13.3) WILD-TYPE   10   34
       clus
vv      AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  ASIAN                           25                             10
  WHITE                           32                             34
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(12P13.33) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 18(12P13.33) MUTATED   29 10
  AMP PEAK 18(12P13.33) WILD-TYPE 38 21
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                             39                              59 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                             10                              21 
$`AMP PEAK 18(12P13.33) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A8O2 
       20.09        20.78         2.63         0.03         0.53         0.46 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4OM 
        0.30         4.31         8.94         3.52         8.78         4.08 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NQ 
        3.32         3.16         2.60         0.36        16.47        21.37 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.36         0.07        10.45         0.33         0.10         0.13 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.10         0.07         0.13         0.10         0.10         0.07 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
        0.07         0.20         1.18         8.02         7.59        14.70 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BW 
        6.35        53.95        14.01 

$`AMP PEAK 18(12P13.33) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       33.27         0.85        20.12         0.26         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.79         0.36         0.13         1.12       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
       60.39        53.85         3.68        41.52        42.77         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16         3.45         3.68         3.35        19.50         6.41 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         7.17         1.38        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49U 
        3.95         3.02        83.24         0.16         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.07         0.07         0.10         0.07         0.10 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
       17.62         5.16         3.78         5.06         7.04        29.59 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78         5.29         4.80 

  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                           0.03                            0.07 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                          53.95                          122.10 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                           2.63                            5.29 
[1] "0.0 - 54.0 (2.6)"  "0.1 - 122.1 (5.3)"
[1] "hr=" "1.1"
D18V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(12P13.33) MUTATED         0        2        1        1        13
  AMP PEAK 18(12P13.33) WILD-TYPE       7        2        3        0        17
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(12P13.33) MUTATED           4         6          3          2
  AMP PEAK 18(12P13.33) WILD-TYPE        12         5          5          4
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 18(12P13.33) MUTATED            3        0
  AMP PEAK 18(12P13.33) WILD-TYPE          0        1
D18V3, multiclass
            clus
vv           AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  STAGE I                                0                               7
  STAGE IA                               2                               2
  STAGE IB                               1                               3
  STAGE II                               1                               0
  STAGE IIA                             13                              17
  STAGE IIB                              4                              12
  STAGE III                              6                               5
  STAGE IIIA                             3                               5
  STAGE IIIB                             2                               4
  STAGE IIIC                             3                               0
  STAGE IV                               0                               1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3+T4
  AMP PEAK 18(12P13.33) MUTATED       3 11    23
  AMP PEAK 18(12P13.33) WILD-TYPE    16 15    27
D18V4, multiclass
       clus
vv      AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  T0+T1                             3                              16
  T2                               11                              15
  T3+T4                            23                              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  AMP PEAK 18(12P13.33) MUTATED   21 10     6
  AMP PEAK 18(12P13.33) WILD-TYPE 29 23     5
D18V5, multiclass
       clus
vv      AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  N0                               21                              29
  N1                               10                              23
  N2+N3                             6                               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1A MX
  AMP PEAK 18(12P13.33) MUTATED   27   0  8
  AMP PEAK 18(12P13.33) WILD-TYPE 48   1  7
D18V6, multiclass
     clus
vv    AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  M0                             27                              48
  M1A                             0                               1
  MX                              8                               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                 cls
clus                               0  1
  AMP PEAK 18(12P13.33) MUTATED    3 39
  AMP PEAK 18(12P13.33) WILD-TYPE 12 51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(12P13.33) MUTATED      3   39
  AMP PEAK 18(12P13.33) WILD-TYPE   12   51
        clus
vv       AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  FEMALE                             3                              12
  MALE                              39                              51
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, binary
                                 cls
clus                               0  1
  AMP PEAK 18(12P13.33) MUTATED   19 22
  AMP PEAK 18(12P13.33) WILD-TYPE 16 44
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(12P13.33) MUTATED     19   22
  AMP PEAK 18(12P13.33) WILD-TYPE   16   44
       clus
vv      AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  ASIAN                            19                              16
  WHITE                            22                              44
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(12P12.1) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 19(12P12.1) MUTATED   30 13
  AMP PEAK 19(12P12.1) WILD-TYPE 37 18
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                            43                             55 
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                            13                             18 
$`AMP PEAK 19(12P12.1) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         2.63        20.12         0.03         0.26         0.53 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30         4.31         3.52         8.78         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A8NJ 
        3.32         4.90        29.00         6.94         0.36        16.47 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       21.37        10.36         0.07        10.45         0.16         0.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.13         0.10         0.07         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN 
        0.10         0.07         0.07         0.20         1.18         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BV 
        7.59         5.06        29.59         6.35        53.95         8.78 
TCGA-S8-A6BW 
       14.01 

$`AMP PEAK 19(12P12.1) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       33.27         0.85        20.78         0.99        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.36         0.13         1.12         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
       60.39        53.85         3.68        41.52        42.77         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        3.16         3.45         8.94         3.68         3.35        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        6.41         7.17         1.38         3.16        30.74         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43         8.71         2.60        25.12         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NU TCGA-LN-A49N TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
        3.02        83.24         0.07         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.13         0.10         0.07         0.10        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB 
        3.78        14.70         7.04         9.30         7.00         5.29 
TCGA-V5-A7RE 
        4.80 

  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                         53.95                         122.10 
  AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE 
                          3.52                           5.16 
[1] "0.0 - 54.0 (3.5)"  "0.1 - 122.1 (5.2)"
[1] "hr=" "1.3"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(12P12.1) MUTATED         0        1        2        1        16
  AMP PEAK 19(12P12.1) WILD-TYPE       7        3        2        0        14
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(12P12.1) MUTATED           5         6          4          2
  AMP PEAK 19(12P12.1) WILD-TYPE        11         5          4          4
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 19(12P12.1) MUTATED            3        1
  AMP PEAK 19(12P12.1) WILD-TYPE          0        0
D19V3, multiclass
            clus
vv           AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  STAGE I                               0                              7
  STAGE IA                              1                              3
  STAGE IB                              2                              2
  STAGE II                              1                              0
  STAGE IIA                            16                             14
  STAGE IIB                             5                             11
  STAGE III                             6                              5
  STAGE IIIA                            4                              4
  STAGE IIIB                            2                              4
  STAGE IIIC                            3                              0
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK 19(12P12.1) MUTATED       3 13    26
  AMP PEAK 19(12P12.1) WILD-TYPE    16 13    24
D19V4, multiclass
       clus
vv      AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  T0+T1                            3                             16
  T2                              13                             13
  T3+T4                           26                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 19(12P12.1) MUTATED   23 14     5
  AMP PEAK 19(12P12.1) WILD-TYPE 27 19     6
D19V5, multiclass
       clus
vv      AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  N0                              23                             27
  N1                              14                             19
  N2+N3                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK 19(12P12.1) MUTATED   31   1  7
  AMP PEAK 19(12P12.1) WILD-TYPE 44   0  8
D19V6, multiclass
     clus
vv    AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  M0                            31                             44
  M1A                            1                              0
  MX                             7                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                              0  1
  AMP PEAK 19(12P12.1) MUTATED    2 46
  AMP PEAK 19(12P12.1) WILD-TYPE 13 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(12P12.1) MUTATED      2   46
  AMP PEAK 19(12P12.1) WILD-TYPE   13   44
        clus
vv       AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  FEMALE                            2                             13
  MALE                             46                             44
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, binary
                                cls
clus                              0  1
  AMP PEAK 19(12P12.1) MUTATED   21 27
  AMP PEAK 19(12P12.1) WILD-TYPE 14 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(12P12.1) MUTATED     21   27
  AMP PEAK 19(12P12.1) WILD-TYPE   14   39
       clus
vv      AMP PEAK 19(12P12.1) MUTATED AMP PEAK 19(12P12.1) WILD-TYPE
  ASIAN                           21                             14
  WHITE                           27                             39
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(13Q22.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(13Q22.1) MUTATED   25  9
  AMP PEAK 20(13Q22.1) WILD-TYPE 42 22
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                            34                             64 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                             9                             22 
$`AMP PEAK 20(13Q22.1) MUTATED`
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43C 
        0.53         0.79       122.10         3.68        42.77         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OQ 
        3.45         8.94         3.35         8.78         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A893 TCGA-LN-A49L 
       30.74         7.13         6.94         0.36         3.02        10.45 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ 
        0.10         0.07         0.10         0.10         0.10         0.10 
TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        1.18         3.78         8.02        14.70         7.04        29.59 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-A7RB 
       53.95         9.30         8.78         5.29 

$`AMP PEAK 20(13Q22.1) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        0.03         0.26         0.99        17.03         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
        1.12         0.46        44.75        60.39        53.85        41.52 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH 
        6.21         0.30         4.31         3.52         3.68        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT 
        6.41         4.08        18.35         3.32         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         8.71         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K 
        3.95        16.47        21.37        83.24        10.36         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X 
        0.16         0.07         0.33         0.13         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.13         0.07         0.10         0.07         0.07 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.20        17.62         5.16         7.59         5.06 
TCGA-R6-A6XQ TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
        6.35         7.00        14.01         4.80 

  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                         4.535                          4.195 
[1] "0.1 - 122.1 (4.5)" "0.0 - 83.2 (4.2)" 
[1] "hr=" "1.4"
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(13Q22.1) MUTATED         4        1        2        1         7
  AMP PEAK 20(13Q22.1) WILD-TYPE       3        3        2        0        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(13Q22.1) MUTATED           3         4          3          1
  AMP PEAK 20(13Q22.1) WILD-TYPE        13         7          5          5
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 20(13Q22.1) MUTATED            1        0
  AMP PEAK 20(13Q22.1) WILD-TYPE          2        1
D20V3, multiclass
            clus
vv           AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  STAGE I                               4                              3
  STAGE IA                              1                              3
  STAGE IB                              2                              2
  STAGE II                              1                              0
  STAGE IIA                             7                             23
  STAGE IIB                             3                             13
  STAGE III                             4                              7
  STAGE IIIA                            3                              5
  STAGE IIIB                            1                              5
  STAGE IIIC                            1                              2
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK 20(13Q22.1) MUTATED       7  9    14
  AMP PEAK 20(13Q22.1) WILD-TYPE    12 17    36
D20V4, multiclass
       clus
vv      AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  T0+T1                            7                             12
  T2                               9                             17
  T3+T4                           14                             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 20(13Q22.1) MUTATED   16 10     4
  AMP PEAK 20(13Q22.1) WILD-TYPE 34 23     7
D20V5, multiclass
       clus
vv      AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  N0                              16                             34
  N1                              10                             23
  N2+N3                            4                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK 20(13Q22.1) MUTATED   22   0  8
  AMP PEAK 20(13Q22.1) WILD-TYPE 53   1  7
D20V6, multiclass
     clus
vv    AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  M0                            22                             53
  M1A                            0                              1
  MX                             8                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                              0  1
  AMP PEAK 20(13Q22.1) MUTATED    6 31
  AMP PEAK 20(13Q22.1) WILD-TYPE  9 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q22.1) MUTATED      6   31
  AMP PEAK 20(13Q22.1) WILD-TYPE    9   59
        clus
vv       AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  FEMALE                            6                              9
  MALE                             31                             59
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, binary
                                cls
clus                              0  1
  AMP PEAK 20(13Q22.1) MUTATED   12 22
  AMP PEAK 20(13Q22.1) WILD-TYPE 23 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q22.1) MUTATED     12   22
  AMP PEAK 20(13Q22.1) WILD-TYPE   23   44
       clus
vv      AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  ASIAN                           12                             23
  WHITE                           22                             44
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(15Q26.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 21(15Q26.3) MUTATED   22 11
  AMP PEAK 21(15Q26.3) WILD-TYPE 45 20
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            33                             65 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            11                             20 
$`AMP PEAK 21(15Q26.3) MUTATED`
TCGA-IG-A50L TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43C TCGA-L5-A4OM 
        0.53       122.10        60.39         3.68         3.16         4.08 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         7.17         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NJ 
        7.13         6.94         2.60         0.36         3.95        16.47 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A5 TCGA-LN-A4MR 
       21.37        10.36        10.45         0.10         0.10         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
       17.62         3.78         7.59        14.70         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BW 
       53.95         9.30        14.01 

$`AMP PEAK 21(15Q26.3) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         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-A625 
        0.03         0.26         0.99        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        0.13         1.12         0.46        44.75        53.85        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       42.77         6.21         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
        3.32         1.38         7.43         8.71        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
        3.02        83.24         0.07         0.16         0.07         0.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.13         0.07         0.10         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.13         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.10         0.20         1.18         5.16         8.02         5.06 
TCGA-R6-A6XG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
       29.59         7.00         8.78         5.29         4.80 

  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                          7.13                           3.32 
[1] "0.1 - 122.1 (7.1)" "0.0 - 83.2 (3.3)" 
[1] "hr=" "1.4"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(15Q26.3) MUTATED         2        3        2        0         9
  AMP PEAK 21(15Q26.3) WILD-TYPE       5        1        2        1        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(15Q26.3) MUTATED           3         4          1          1
  AMP PEAK 21(15Q26.3) WILD-TYPE        13         7          7          5
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 21(15Q26.3) MUTATED            1        1
  AMP PEAK 21(15Q26.3) WILD-TYPE          2        0
D21V3, multiclass
            clus
vv           AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  STAGE I                               2                              5
  STAGE IA                              3                              1
  STAGE IB                              2                              2
  STAGE II                              0                              1
  STAGE IIA                             9                             21
  STAGE IIB                             3                             13
  STAGE III                             4                              7
  STAGE IIIA                            1                              7
  STAGE IIIB                            1                              5
  STAGE IIIC                            1                              2
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK 21(15Q26.3) MUTATED       7  9    13
  AMP PEAK 21(15Q26.3) WILD-TYPE    12 17    37
D21V4, multiclass
       clus
vv      AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  T0+T1                            7                             12
  T2                               9                             17
  T3+T4                           13                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 21(15Q26.3) MUTATED   17 10     2
  AMP PEAK 21(15Q26.3) WILD-TYPE 33 23     9
D21V5, multiclass
       clus
vv      AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  N0                              17                             33
  N1                              10                             23
  N2+N3                            2                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK 21(15Q26.3) MUTATED   19   1  7
  AMP PEAK 21(15Q26.3) WILD-TYPE 56   0  8
D21V6, multiclass
     clus
vv    AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  M0                            19                             56
  M1A                            1                              0
  MX                             7                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                              0  1
  AMP PEAK 21(15Q26.3) MUTATED    5 31
  AMP PEAK 21(15Q26.3) WILD-TYPE 10 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      5   31
  AMP PEAK 21(15Q26.3) WILD-TYPE   10   59
        clus
vv       AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  FEMALE                            5                             10
  MALE                             31                             59
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, binary
                                cls
clus                              0  1
  AMP PEAK 21(15Q26.3) MUTATED    8 26
  AMP PEAK 21(15Q26.3) WILD-TYPE 27 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      8   26
  AMP PEAK 21(15Q26.3) WILD-TYPE   27   40
       clus
vv      AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  ASIAN                            8                             27
  WHITE                           26                             40
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(17Q12) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 22(17Q12) MUTATED   26 11
  AMP PEAK 22(17Q12) WILD-TYPE 41 20
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                          37                           61 
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                          11                           20 
$`AMP PEAK 22(17Q12) MUTATED`
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FB TCGA-L5-A43E 
       20.09         0.53        17.03         0.36        60.39         3.45 
TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.30         3.52        18.35         3.32         1.38        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NJ 
        4.90        29.00         7.13         2.60         7.40        16.47 
TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 
       10.45         0.10         0.13         0.07         0.10         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         0.10         0.07        17.62         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BW 
        7.59         5.06         7.04        29.59        53.95        14.01 
TCGA-V5-A7RE 
        4.80 

$`AMP PEAK 22(17Q12) WILD-TYPE`
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         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.26         0.99         0.79         0.13         1.12         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        53.85         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        6.21         3.16         4.31         8.94         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
       19.50         8.78         6.41         4.08         7.17         3.16 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 
        7.43         6.94         8.71        25.12         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
        3.02        21.37        83.24        10.36         0.07         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A5 
        0.07         0.33         0.07         0.10         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.10         0.07         0.20         1.18 
TCGA-Q9-A6FU TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        5.16        14.70         6.35         9.30         7.00         8.78 
TCGA-V5-A7RB 
        5.29 

  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                       60.39                       122.10 
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                        4.90                         3.95 
[1] "0.1 - 60.4 (4.9)"  "0.0 - 122.1 (4.0)"
[1] "hr=" "1.1"
D22V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(17Q12) MUTATED         2        0        2        0        10
  AMP PEAK 22(17Q12) WILD-TYPE       5        4        2        1        20
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(17Q12) MUTATED           5         6          2          3
  AMP PEAK 22(17Q12) WILD-TYPE        11         5          6          3
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 22(17Q12) MUTATED            1        1
  AMP PEAK 22(17Q12) WILD-TYPE          2        0
D22V3, multiclass
            clus
vv           AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  STAGE I                             2                            5
  STAGE IA                            0                            4
  STAGE IB                            2                            2
  STAGE II                            0                            1
  STAGE IIA                          10                           20
  STAGE IIB                           5                           11
  STAGE III                           6                            5
  STAGE IIIA                          2                            6
  STAGE IIIB                          3                            3
  STAGE IIIC                          1                            2
  STAGE IV                            1                            0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3+T4
  AMP PEAK 22(17Q12) MUTATED       6  7    19
  AMP PEAK 22(17Q12) WILD-TYPE    13 19    31
D22V4, multiclass
       clus
vv      AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  T0+T1                          6                           13
  T2                             7                           19
  T3+T4                         19                           31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2+N3
  AMP PEAK 22(17Q12) MUTATED   14 13     5
  AMP PEAK 22(17Q12) WILD-TYPE 36 20     6
D22V5, multiclass
       clus
vv      AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  N0                            14                           36
  N1                            13                           20
  N2+N3                          5                            6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1A MX
  AMP PEAK 22(17Q12) MUTATED   26   1  3
  AMP PEAK 22(17Q12) WILD-TYPE 49   0 12
D22V6, multiclass
     clus
vv    AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  M0                          26                           49
  M1A                          1                            0
  MX                           3                           12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                              cls
clus                            0  1
  AMP PEAK 22(17Q12) MUTATED    4 34
  AMP PEAK 22(17Q12) WILD-TYPE 11 56
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(17Q12) MUTATED      4   34
  AMP PEAK 22(17Q12) WILD-TYPE   11   56
        clus
vv       AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  FEMALE                          4                           11
  MALE                           34                           56
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, binary
                              cls
clus                            0  1
  AMP PEAK 22(17Q12) MUTATED   12 24
  AMP PEAK 22(17Q12) WILD-TYPE 23 42
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(17Q12) MUTATED     12   24
  AMP PEAK 22(17Q12) WILD-TYPE   23   42
       clus
vv      AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  ASIAN                         12                           23
  WHITE                         24                           42
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(18P11.32) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 23(18P11.32) MUTATED   24 11
  AMP PEAK 23(18P11.32) WILD-TYPE 43 20
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                             35                              63 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                             11                              20 
$`AMP PEAK 23(18P11.32) MUTATED`
TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43C 
        0.53         0.36        44.75        60.39         3.68         3.16 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.31         8.94         4.08         3.32         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NQ TCGA-L7-A6VZ 
        4.90         7.13         2.60         0.36        21.37        10.36 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.33         0.13         0.07         0.10         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 
        0.07         0.07         0.10         0.10         0.07         1.18 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RE 
        8.02         5.06        53.95        14.01         4.80 

$`AMP PEAK 23(18P11.32) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         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-A6QS 
        0.03         0.26         0.99        17.03         0.79         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
        1.12         0.46       122.10        53.85        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        6.21         3.45         0.30         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS 
       19.50         8.78         6.41        18.35         7.17        30.74 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L 
        3.95         3.02        16.47        83.24         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.16         0.07         0.10         0.13         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.07         0.20        17.62         5.16         3.78 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59        14.70         7.04        29.59         6.35         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        7.00         8.78         5.29 

  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                           0.07                            0.03 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                          60.39                          122.10 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                           3.16                            6.41 
[1] "0.1 - 60.4 (3.2)"  "0.0 - 122.1 (6.4)"
[1] "hr=" "1.5"
D23V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(18P11.32) MUTATED         1        2        2        0        11
  AMP PEAK 23(18P11.32) WILD-TYPE       6        2        2        1        19
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(18P11.32) MUTATED           3         7          2          1
  AMP PEAK 23(18P11.32) WILD-TYPE        13         4          6          5
                                 vv
clus                              STAGE IIIC STAGE IV
  AMP PEAK 23(18P11.32) MUTATED            2        1
  AMP PEAK 23(18P11.32) WILD-TYPE          1        0
D23V3, multiclass
            clus
vv           AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  STAGE I                                1                               6
  STAGE IA                               2                               2
  STAGE IB                               2                               2
  STAGE II                               0                               1
  STAGE IIA                             11                              19
  STAGE IIB                              3                              13
  STAGE III                              7                               4
  STAGE IIIA                             2                               6
  STAGE IIIB                             1                               5
  STAGE IIIC                             2                               1
  STAGE IV                               1                               0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3+T4
  AMP PEAK 23(18P11.32) MUTATED       5  8    21
  AMP PEAK 23(18P11.32) WILD-TYPE    14 18    29
D23V4, multiclass
       clus
vv      AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  T0+T1                             5                              14
  T2                                8                              18
  T3+T4                            21                              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  AMP PEAK 23(18P11.32) MUTATED   18 11     5
  AMP PEAK 23(18P11.32) WILD-TYPE 32 22     6
D23V5, multiclass
       clus
vv      AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  N0                               18                              32
  N1                               11                              22
  N2+N3                             5                               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1A MX
  AMP PEAK 23(18P11.32) MUTATED   24   1  8
  AMP PEAK 23(18P11.32) WILD-TYPE 51   0  7
D23V6, multiclass
     clus
vv    AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  M0                             24                              51
  M1A                             1                               0
  MX                              8                               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                 cls
clus                               0  1
  AMP PEAK 23(18P11.32) MUTATED    3 35
  AMP PEAK 23(18P11.32) WILD-TYPE 12 55
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED      3   35
  AMP PEAK 23(18P11.32) WILD-TYPE   12   55
        clus
vv       AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  FEMALE                             3                              12
  MALE                              35                              55
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, binary
                                 cls
clus                               0  1
  AMP PEAK 23(18P11.32) MUTATED   18 18
  AMP PEAK 23(18P11.32) WILD-TYPE 17 48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED     18   18
  AMP PEAK 23(18P11.32) WILD-TYPE   17   48
       clus
vv      AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  ASIAN                            18                              17
  WHITE                            18                              48
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(18Q11.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 24(18Q11.2) MUTATED   20  9
  AMP PEAK 24(18Q11.2) WILD-TYPE 47 22
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                            29                             69 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                             9                             22 
$`AMP PEAK 24(18Q11.2) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-IG-A625 TCGA-JY-A6FB TCGA-L5-A43E TCGA-L5-A43M 
       33.27         0.03         0.36        60.39         3.45         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
        3.52         3.35         4.08        18.35         3.32         3.16 
TCGA-L5-A88Y TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49X TCGA-LN-A4A3 
        0.36        83.24        10.36         0.07         0.10         0.07 
TCGA-LN-A4A4 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.10         0.10         0.20         3.78         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE 
        7.04        29.59         8.78        14.01         4.80 

$`AMP PEAK 24(18Q11.2) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       20.09         0.85        20.78         2.63        20.12         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99         0.53        17.03         0.79         0.13         1.12 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.46       122.10        44.75        53.85         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF 
       42.77         6.21         3.16         0.30         4.31         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       19.50         8.78         6.41         7.17         1.38        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        2.60        25.12         7.40         3.95         3.02        16.47 
TCGA-L5-A8NQ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       21.37        10.45         0.16         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
        0.13         0.07         0.10         0.07         0.07         0.13 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 
        0.10         0.10         0.07         0.07         0.07         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 
       17.62         5.16         8.02        14.70         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB 
        9.30         7.00         5.29 

  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                         83.24                         122.10 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                          3.78                           4.90 
[1] "0.0 - 83.2 (3.8)"  "0.1 - 122.1 (4.9)"
[1] "hr=" "1"  
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(18Q11.2) MUTATED         3        2        2        0         5
  AMP PEAK 24(18Q11.2) WILD-TYPE       4        2        2        1        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(18Q11.2) MUTATED           3         3          1          3
  AMP PEAK 24(18Q11.2) WILD-TYPE        13         8          7          3
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 24(18Q11.2) MUTATED            2        0
  AMP PEAK 24(18Q11.2) WILD-TYPE          1        1
D24V3, multiclass
            clus
vv           AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  STAGE I                               3                              4
  STAGE IA                              2                              2
  STAGE IB                              2                              2
  STAGE II                              0                              1
  STAGE IIA                             5                             25
  STAGE IIB                             3                             13
  STAGE III                             3                              8
  STAGE IIIA                            1                              7
  STAGE IIIB                            3                              3
  STAGE IIIC                            2                              1
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK 24(18Q11.2) MUTATED       8  5    13
  AMP PEAK 24(18Q11.2) WILD-TYPE    11 21    37
D24V4, multiclass
       clus
vv      AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  T0+T1                            8                             11
  T2                               5                             21
  T3+T4                           13                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 24(18Q11.2) MUTATED   13  7     6
  AMP PEAK 24(18Q11.2) WILD-TYPE 37 26     5
D24V5, multiclass
       clus
vv      AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  N0                              13                             37
  N1                               7                             26
  N2+N3                            6                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK 24(18Q11.2) MUTATED   17   0  6
  AMP PEAK 24(18Q11.2) WILD-TYPE 58   1  9
D24V6, multiclass
     clus
vv    AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  M0                            17                             58
  M1A                            0                              1
  MX                             6                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                cls
clus                              0  1
  AMP PEAK 24(18Q11.2) MUTATED    5 25
  AMP PEAK 24(18Q11.2) WILD-TYPE 10 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      5   25
  AMP PEAK 24(18Q11.2) WILD-TYPE   10   65
        clus
vv       AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  FEMALE                            5                             10
  MALE                             25                             65
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, binary
                                cls
clus                              0  1
  AMP PEAK 24(18Q11.2) MUTATED    8 21
  AMP PEAK 24(18Q11.2) WILD-TYPE 27 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      8   21
  AMP PEAK 24(18Q11.2) WILD-TYPE   27   45
       clus
vv      AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  ASIAN                            8                             27
  WHITE                           21                             45
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(19P13.2) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 25(19P13.2) MUTATED   14  3
  AMP PEAK 25(19P13.2) WILD-TYPE 53 28
  AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE 
                            17                             81 
  AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE 
                             3                             28 
$`AMP PEAK 25(19P13.2) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A51D TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A4OR 
       20.09        20.12        17.03         3.16         4.31         3.16 
TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-LN-A49K TCGA-LN-A49O 
       29.00         2.60         0.36         3.95         0.07         0.33 
TCGA-LN-A49V TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-S8-A6BW 
        0.10         0.07         0.10         1.18        14.01 

$`AMP PEAK 25(19P13.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78         2.63         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99         0.53         0.79         0.36         0.13         1.12 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.46       122.10        44.75        60.39        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       41.52        42.77         6.21         3.45         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        4.08        18.35         3.32         7.17         1.38        30.74 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        4.90         7.13         7.43         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.40         3.02        16.47        21.37        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45         0.16         0.07         0.10         0.13         0.07 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.10         0.07         0.13         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 
        0.07         0.07         0.10         0.07         0.20        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         3.78         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.04        29.59         6.35        53.95         9.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        8.78         5.29         4.80 

  AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE 
                          29.0                          122.1 
  AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE 
                          3.16                           5.06 
[1] "0.1 - 29.0 (3.2)"  "0.0 - 122.1 (5.1)"
[1] "hr=" "1.4"
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(19P13.2) MUTATED         0        1        1        1         7
  AMP PEAK 25(19P13.2) WILD-TYPE       7        3        3        0        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(19P13.2) MUTATED           3         2          1          0
  AMP PEAK 25(19P13.2) WILD-TYPE        13         9          7          6
                                vv
clus                             STAGE IIIC STAGE IV
  AMP PEAK 25(19P13.2) MUTATED            0        0
  AMP PEAK 25(19P13.2) WILD-TYPE          3        1
D25V3, multiclass
            clus
vv           AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE
  STAGE I                               0                              7
  STAGE IA                              1                              3
  STAGE IB                              1                              3
  STAGE II                              1                              0
  STAGE IIA                             7                             23
  STAGE IIB                             3                             13
  STAGE III                             2                              9
  STAGE IIIA                            1                              7
  STAGE IIIB                            0                              6
  STAGE IIIC                            0                              3
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  AMP PEAK 25(19P13.2) MUTATED       3  4    11
  AMP PEAK 25(19P13.2) WILD-TYPE    16 22    39
D25V4, multiclass
       clus
vv      AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE
  T0+T1                            3                             16
  T2                               4                             22
  T3+T4                           11                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 25(19P13.2) MUTATED   13  5     0
  AMP PEAK 25(19P13.2) WILD-TYPE 37 28    11
D25V5, multiclass
       clus
vv      AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE
  N0                              13                             37
  N1                               5                             28
  N2+N3                            0                             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  AMP PEAK 25(19P13.2) MUTATED   13   0  5
  AMP PEAK 25(19P13.2) WILD-TYPE 62   1 10
D25V6, multiclass
     clus
vv    AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE
  M0                            13                             62
  M1A                            0                              1
  MX                             5                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                                cls
clus                              0  1
  AMP PEAK 25(19P13.2) MUTATED    0 19
  AMP PEAK 25(19P13.2) WILD-TYPE 15 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(19P13.2) MUTATED      0   19
  AMP PEAK 25(19P13.2) WILD-TYPE   15   71
        clus
vv       AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE
  FEMALE                            0                             15
  MALE                             19                             71
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, binary
                                cls
clus                              0  1
  AMP PEAK 25(19P13.2) MUTATED    8 11
  AMP PEAK 25(19P13.2) WILD-TYPE 27 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(19P13.2) MUTATED      8   11
  AMP PEAK 25(19P13.2) WILD-TYPE   27   55
       clus
vv      AMP PEAK 25(19P13.2) MUTATED AMP PEAK 25(19P13.2) WILD-TYPE
  ASIAN                            8                             27
  WHITE                           11                             55
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(19Q12) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 26(19Q12) MUTATED   18  7
  AMP PEAK 26(19Q12) WILD-TYPE 49 24
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                          25                           73 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                           7                           24 
$`AMP PEAK 26(19Q12) MUTATED`
TCGA-IG-A3QL TCGA-IG-A4QS TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OF 
       20.09         0.26        42.77         3.16         3.52         3.68 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       19.50        18.35         3.32         1.38         3.16        30.74 
TCGA-L5-A891 TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A4A4 
        3.95        10.36         0.07        10.45         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 
        0.10         0.10         5.06        14.70        29.59        53.95 
TCGA-S8-A6BW 
       14.01 

$`AMP PEAK 26(19Q12) WILD-TYPE`
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         0.03 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.99         0.53        17.03         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        1.12         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52         6.21         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP 
        8.94         3.35         8.78         6.41         4.08         7.17 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NJ 
        2.60        25.12         0.36         7.40         3.02        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       21.37        83.24         0.16         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.13         0.10         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.07         0.07         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        1.18        17.62         5.16         3.78         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        7.04         6.35         9.30         7.00         8.78         5.29 
TCGA-V5-A7RE 
        4.80 

  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                       53.95                       122.10 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                        3.95                         4.31 
[1] "0.1 - 54.0 (4.0)"  "0.0 - 122.1 (4.3)"
[1] "hr=" "1.3"
D26V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(19Q12) MUTATED         1        1        1        1         6
  AMP PEAK 26(19Q12) WILD-TYPE       6        3        3        0        24
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(19Q12) MUTATED           5         1          1          2
  AMP PEAK 26(19Q12) WILD-TYPE        11        10          7          4
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 26(19Q12) MUTATED            2        0
  AMP PEAK 26(19Q12) WILD-TYPE          1        1
D26V3, multiclass
            clus
vv           AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  STAGE I                             1                            6
  STAGE IA                            1                            3
  STAGE IB                            1                            3
  STAGE II                            1                            0
  STAGE IIA                           6                           24
  STAGE IIB                           5                           11
  STAGE III                           1                           10
  STAGE IIIA                          1                            7
  STAGE IIIB                          2                            4
  STAGE IIIC                          2                            1
  STAGE IV                            0                            1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3+T4
  AMP PEAK 26(19Q12) MUTATED       4  8    10
  AMP PEAK 26(19Q12) WILD-TYPE    15 18    40
D26V4, multiclass
       clus
vv      AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  T0+T1                          4                           15
  T2                             8                           18
  T3+T4                         10                           40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2+N3
  AMP PEAK 26(19Q12) MUTATED   11  6     5
  AMP PEAK 26(19Q12) WILD-TYPE 39 27     6
D26V5, multiclass
       clus
vv      AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  N0                            11                           39
  N1                             6                           27
  N2+N3                          5                            6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1A MX
  AMP PEAK 26(19Q12) MUTATED   15   0  4
  AMP PEAK 26(19Q12) WILD-TYPE 60   1 11
D26V6, multiclass
     clus
vv    AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  M0                          15                           60
  M1A                          0                            1
  MX                           4                           11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                              cls
clus                            0  1
  AMP PEAK 26(19Q12) MUTATED    1 26
  AMP PEAK 26(19Q12) WILD-TYPE 14 64
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(19Q12) MUTATED      1   26
  AMP PEAK 26(19Q12) WILD-TYPE   14   64
        clus
vv       AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  FEMALE                          1                           14
  MALE                           26                           64
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, binary
                              cls
clus                            0  1
  AMP PEAK 26(19Q12) MUTATED    8 19
  AMP PEAK 26(19Q12) WILD-TYPE 27 47
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(19Q12) MUTATED      8   19
  AMP PEAK 26(19Q12) WILD-TYPE   27   47
       clus
vv      AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  ASIAN                          8                           27
  WHITE                         19                           47
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  1(1P36.13) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.13) MUTATED   19 13
  DEL PEAK  1(1P36.13) WILD-TYPE 48 18
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            32                             66 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            13                             18 
$`DEL PEAK  1(1P36.13) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 
       33.27        20.09         0.03         0.26         0.53         0.36 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
      122.10        60.39         0.30         4.31         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.68         3.35         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-LN-A49K 
        7.13         7.43         2.60         7.40        16.47         0.07 
TCGA-LN-A49R TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.10         0.20         1.18         8.02         7.59         5.06 
TCGA-S8-A6BW TCGA-V5-A7RE 
       14.01         4.80 

$`DEL PEAK  1(1P36.13) WILD-TYPE`
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D 
        0.85        20.78         2.63        20.12         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD 
        0.79         0.13         1.12         0.46        44.75        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         6.21         3.16         3.45 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       19.50         8.78         6.41         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        7.17         1.38         6.94         8.71        25.12         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L 
        3.95         3.02        21.37        83.24        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.16         0.07         0.33         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.07         0.07         0.10         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       17.62         5.16         3.78        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        6.35        53.95         9.30         7.00         8.78         5.29 

  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                         4.850                          3.865 
[1] "0.0 - 122.1 (4.8)" "0.1 - 83.2 (3.9)" 
[1] "hr=" "1.4"
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.13) MUTATED         3        1        2        0         7
  DEL PEAK  1(1P36.13) WILD-TYPE       4        3        2        1        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.13) MUTATED           8         5          1          3
  DEL PEAK  1(1P36.13) WILD-TYPE         8         6          7          3
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK  1(1P36.13) MUTATED            0        1
  DEL PEAK  1(1P36.13) WILD-TYPE          3        0
D27V3, multiclass
            clus
vv           DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  STAGE I                               3                              4
  STAGE IA                              1                              3
  STAGE IB                              2                              2
  STAGE II                              0                              1
  STAGE IIA                             7                             23
  STAGE IIB                             8                              8
  STAGE III                             5                              6
  STAGE IIIA                            1                              7
  STAGE IIIB                            3                              3
  STAGE IIIC                            0                              3
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK  1(1P36.13) MUTATED       7  9    16
  DEL PEAK  1(1P36.13) WILD-TYPE    12 17    34
D27V4, multiclass
       clus
vv      DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  T0+T1                            7                             12
  T2                               9                             17
  T3+T4                           16                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK  1(1P36.13) MUTATED   14 14     4
  DEL PEAK  1(1P36.13) WILD-TYPE 36 19     7
D27V5, multiclass
       clus
vv      DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  N0                              14                             36
  N1                              14                             19
  N2+N3                            4                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK  1(1P36.13) MUTATED   24   1  5
  DEL PEAK  1(1P36.13) WILD-TYPE 51   0 10
D27V6, multiclass
     clus
vv    DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  M0                            24                             51
  M1A                            1                              0
  MX                             5                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.13) MUTATED    7 28
  DEL PEAK  1(1P36.13) WILD-TYPE  8 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED      7   28
  DEL PEAK  1(1P36.13) WILD-TYPE    8   62
        clus
vv       DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  FEMALE                            7                              8
  MALE                             28                             62
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.13) MUTATED    9 24
  DEL PEAK  1(1P36.13) WILD-TYPE 26 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED      9   24
  DEL PEAK  1(1P36.13) WILD-TYPE   26   42
       clus
vv      DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  ASIAN                            9                             26
  WHITE                           24                             42
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P13.2) MUTATED   23 10
  DEL PEAK  2(1P13.2) WILD-TYPE 44 21
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           33                            65 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           10                            21 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       33.27        20.09         2.63         0.03         0.26         0.53 
TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-JY-A6FE TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
        0.79         0.46         3.68         0.30         8.94         3.52 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.35        19.50         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-LN-A49K 
        6.94         2.60         0.36         7.40        16.47         0.07 
TCGA-LN-A49W TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.10         0.07         0.20         1.18        17.62 
TCGA-R6-A6DQ TCGA-R6-A6Y0 TCGA-S8-A6BW 
        7.59        53.95        14.01 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
        0.85        20.78        20.12         0.99        17.03         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12       122.10        44.75        60.39        53.85 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J 
       41.52        42.77         6.21         3.16         3.45         4.31 
TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.68         8.78         6.41         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88T TCGA-L5-A88W 
        7.17         1.38         3.16        30.74         8.71        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L 
        3.95         3.02        21.37        83.24        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.16         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
        0.10         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.07         0.10         0.07         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78         5.29         4.80 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        53.95                        122.10 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         3.52                          4.80 
[1] "0.0 - 54.0 (3.5)"  "0.1 - 122.1 (4.8)"
[1] "hr=" "1.2"
D28V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED         2        0        3        0        11
  DEL PEAK  2(1P13.2) WILD-TYPE       5        4        1        1        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED           5         6          2          3
  DEL PEAK  2(1P13.2) WILD-TYPE        11         5          6          3
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  2(1P13.2) MUTATED            0        1
  DEL PEAK  2(1P13.2) WILD-TYPE          3        0
D28V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              2                             5
  STAGE IA                             0                             4
  STAGE IB                             3                             1
  STAGE II                             0                             1
  STAGE IIA                           11                            19
  STAGE IIB                            5                            11
  STAGE III                            6                             5
  STAGE IIIA                           2                             6
  STAGE IIIB                           3                             3
  STAGE IIIC                           0                             3
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK  2(1P13.2) MUTATED       4 10    21
  DEL PEAK  2(1P13.2) WILD-TYPE    15 16    29
D28V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T0+T1                           4                            15
  T2                             10                            16
  T3+T4                          21                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  2(1P13.2) MUTATED   17 14     4
  DEL PEAK  2(1P13.2) WILD-TYPE 33 19     7
D28V5, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                             17                            33
  N1                             14                            19
  N2+N3                           4                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK  2(1P13.2) MUTATED   28   1  5
  DEL PEAK  2(1P13.2) WILD-TYPE 47   0 10
D28V6, multiclass
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  M0                           28                            47
  M1A                           1                             0
  MX                            5                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    6 31
  DEL PEAK  2(1P13.2) WILD-TYPE  9 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6   31
  DEL PEAK  2(1P13.2) WILD-TYPE    9   59
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                           6                             9
  MALE                            31                            59
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   12 22
  DEL PEAK  2(1P13.2) WILD-TYPE 23 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     12   22
  DEL PEAK  2(1P13.2) WILD-TYPE   23   44
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                          12                            23
  WHITE                          22                            44
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(1Q44) MUTATED    9  4
  DEL PEAK  3(1Q44) WILD-TYPE 58 27
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         13                          85 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          4                          27 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-IG-A4QS TCGA-IG-A6QS TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A8NU 
        0.26         0.13         3.52         6.41         3.32        83.24 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-R6-A6DQ 
       10.36         0.07         0.33         0.07         0.10         7.59 
TCGA-R6-A6Y0 
       53.95 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         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 
        0.03         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        1.12         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         8.94         3.68         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        8.78         4.08        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 
       30.74         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        3.02        16.47        21.37        10.45         0.16         0.07 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10         0.13         0.07         0.10         0.07         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.13         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.07         0.20         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        3.78         8.02         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        6.35         9.30         7.00         8.78        14.01         5.29 
TCGA-V5-A7RE 
        4.80 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       0.07                        0.03 
  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 
                       3.32                        4.80 
[1] "0.1 - 83.2 (3.3)"  "0.0 - 122.1 (4.8)"
[1] "hr=" "1.1"
D29V2, 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       6        4        4        1        24
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q44) MUTATED           1         0          0          2
  DEL PEAK  3(1Q44) WILD-TYPE        15        11          8          4
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  3(1Q44) MUTATED            2        0
  DEL PEAK  3(1Q44) WILD-TYPE          1        1
D29V3, multiclass
            clus
vv           DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                            1                           6
  STAGE IA                           0                           4
  STAGE IB                           0                           4
  STAGE II                           0                           1
  STAGE IIA                          6                          24
  STAGE IIB                          1                          15
  STAGE III                          0                          11
  STAGE IIIA                         0                           8
  STAGE IIIB                         2                           4
  STAGE IIIC                         2                           1
  STAGE IV                           0                           1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3+T4
  DEL PEAK  3(1Q44) MUTATED       1  4     7
  DEL PEAK  3(1Q44) WILD-TYPE    18 22    43
D29V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T0+T1                         1                          18
  T2                            4                          22
  T3+T4                         7                          43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2+N3
  DEL PEAK  3(1Q44) MUTATED    7  1     4
  DEL PEAK  3(1Q44) WILD-TYPE 43 32     7
D29V5, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                            7                          43
  N1                            1                          32
  N2+N3                         4                           7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1A MX
  DEL PEAK  3(1Q44) MUTATED   10   0  1
  DEL PEAK  3(1Q44) WILD-TYPE 65   1 14
D29V6, multiclass
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  M0                         10                          65
  M1A                         0                           1
  MX                          1                          14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q44) MUTATED    2 12
  DEL PEAK  3(1Q44) WILD-TYPE 13 78
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      2   12
  DEL PEAK  3(1Q44) WILD-TYPE   13   78
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                         2                          13
  MALE                          12                          78
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q44) MUTATED    5  9
  DEL PEAK  3(1Q44) WILD-TYPE 30 57
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      5    9
  DEL PEAK  3(1Q44) WILD-TYPE   30   57
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                         5                          30
  WHITE                         9                          57
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q22.1) MUTATED   20 10
  DEL PEAK  4(2Q22.1) WILD-TYPE 47 21
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           30                            68 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           10                            21 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
       33.27         0.85         2.63        20.12         0.03         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD 
       17.03         0.79         0.13         0.46        44.75        53.85 
TCGA-JY-A6FG TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OS TCGA-L5-A4OX 
       41.52         3.16         0.30         3.52        30.74         7.43 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ 
        7.40         3.02        10.36        10.45         0.07         0.10 
TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RB 
        0.20         5.16        29.59        53.95        14.01         5.29 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP 
       20.09        20.78         0.26         0.99         0.36         1.12 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E 
      122.10        60.39         3.68        42.77         6.21         3.45 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        4.31         8.94         3.68         3.35        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        6.41         4.08        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T 
        3.16         4.90        29.00         7.13         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NQ 
        2.60        25.12         0.36         3.95        16.47        21.37 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       83.24         0.07         0.16         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 
        0.13         0.07         0.10         0.07         0.10         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07         1.18        17.62         3.78         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        5.06        14.70         7.04         6.35         9.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RE 
        8.78         4.80 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        53.95                        122.10 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        5.225                         4.015 
[1] "0.0 - 54.0 (5.2)"  "0.1 - 122.1 (4.0)"
[1] "hr=" "1.2"
D30V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(2Q22.1) MUTATED         1        0        2        0         9
  DEL PEAK  4(2Q22.1) WILD-TYPE       6        4        2        1        21
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2Q22.1) MUTATED           7         3          4          3
  DEL PEAK  4(2Q22.1) WILD-TYPE         9         8          4          3
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  4(2Q22.1) MUTATED            1        0
  DEL PEAK  4(2Q22.1) WILD-TYPE          2        1
D30V3, multiclass
            clus
vv           DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  STAGE I                              1                             6
  STAGE IA                             0                             4
  STAGE IB                             2                             2
  STAGE II                             0                             1
  STAGE IIA                            9                            21
  STAGE IIB                            7                             9
  STAGE III                            3                             8
  STAGE IIIA                           4                             4
  STAGE IIIB                           3                             3
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK  4(2Q22.1) MUTATED       4 12    15
  DEL PEAK  4(2Q22.1) WILD-TYPE    15 14    35
D30V4, multiclass
       clus
vv      DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T0+T1                           4                            15
  T2                             12                            14
  T3+T4                          15                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  4(2Q22.1) MUTATED   12 15     4
  DEL PEAK  4(2Q22.1) WILD-TYPE 38 18     7
D30V5, multiclass
       clus
vv      DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                             12                            38
  N1                             15                            18
  N2+N3                           4                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK  4(2Q22.1) MUTATED   27   0  3
  DEL PEAK  4(2Q22.1) WILD-TYPE 48   1 12
D30V6, multiclass
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  M0                           27                            48
  M1A                           0                             1
  MX                            3                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED    6 28
  DEL PEAK  4(2Q22.1) WILD-TYPE  9 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      6   28
  DEL PEAK  4(2Q22.1) WILD-TYPE    9   62
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                           6                             9
  MALE                            28                            62
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED   12 21
  DEL PEAK  4(2Q22.1) WILD-TYPE 23 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     12   21
  DEL PEAK  4(2Q22.1) WILD-TYPE   23   45
       clus
vv      DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  ASIAN                          12                            23
  WHITE                          21                            45
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  5(2Q33.3) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q33.3) MUTATED   11  6
  DEL PEAK  5(2Q33.3) WILD-TYPE 56 25
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           17                            81 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                            6                            25 
$`DEL PEAK  5(2Q33.3) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 
       20.09         0.85         2.63        20.12         0.03         0.79 
TCGA-JY-A6FD TCGA-L5-A43H TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A893 TCGA-L5-A8NJ 
       53.85         0.30        30.74         6.94         3.02        16.47 
TCGA-LN-A49K TCGA-LN-A49V TCGA-LN-A4MQ TCGA-R6-A6DN TCGA-S8-A6BV 
        0.07         0.10         0.10         8.02         8.78 

$`DEL PEAK  5(2Q33.3) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       33.27        20.78         0.26         0.99         0.53        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.36         0.13         1.12         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       60.39         3.68        41.52        42.77         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.45         4.31         8.94         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       19.50         8.78         6.41         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.43         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        3.95        21.37        83.24        10.36        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        0.07         0.33         0.10         0.13         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.07         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       17.62         5.16         3.78         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.04        29.59         6.35        53.95         9.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       14.01         5.29         4.80 

  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                        53.85                        122.10 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                         3.02                          4.31 
[1] "0.0 - 53.9 (3.0)"  "0.1 - 122.1 (4.3)"
[1] "hr=" "1.2"
D31V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q33.3) MUTATED         1        0        2        0         6
  DEL PEAK  5(2Q33.3) WILD-TYPE       6        4        2        1        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q33.3) MUTATED           3         3          4          0
  DEL PEAK  5(2Q33.3) WILD-TYPE        13         8          4          6
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  5(2Q33.3) MUTATED            0        0
  DEL PEAK  5(2Q33.3) WILD-TYPE          3        1
D31V3, multiclass
            clus
vv           DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  STAGE I                              1                             6
  STAGE IA                             0                             4
  STAGE IB                             2                             2
  STAGE II                             0                             1
  STAGE IIA                            6                            24
  STAGE IIB                            3                            13
  STAGE III                            3                             8
  STAGE IIIA                           4                             4
  STAGE IIIB                           0                             6
  STAGE IIIC                           0                             3
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK  5(2Q33.3) MUTATED       1  5    13
  DEL PEAK  5(2Q33.3) WILD-TYPE    18 21    37
D31V4, multiclass
       clus
vv      DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  T0+T1                           1                            18
  T2                              5                            21
  T3+T4                          13                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  5(2Q33.3) MUTATED   11  8     0
  DEL PEAK  5(2Q33.3) WILD-TYPE 39 25    11
D31V5, multiclass
       clus
vv      DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  N0                             11                            39
  N1                              8                            25
  N2+N3                           0                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK  5(2Q33.3) MUTATED   17   0  2
  DEL PEAK  5(2Q33.3) WILD-TYPE 58   1 13
D31V6, multiclass
     clus
vv    DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  M0                           17                            58
  M1A                           0                             1
  MX                            2                            13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q33.3) MUTATED    3 17
  DEL PEAK  5(2Q33.3) WILD-TYPE 12 73
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED      3   17
  DEL PEAK  5(2Q33.3) WILD-TYPE   12   73
        clus
vv       DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  FEMALE                           3                            12
  MALE                            17                            73
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q33.3) MUTATED    7 13
  DEL PEAK  5(2Q33.3) WILD-TYPE 28 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED      7   13
  DEL PEAK  5(2Q33.3) WILD-TYPE   28   53
       clus
vv      DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  ASIAN                           7                            28
  WHITE                          13                            53
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  6(3P25.3) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(3P25.3) MUTATED   43 13
  DEL PEAK  6(3P25.3) WILD-TYPE 24 18
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                           56                            42 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                           13                            18 
$`DEL PEAK  6(3P25.3) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6FB 
        0.26         0.53        17.03         0.79         0.13        60.39 
TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
       53.85         3.45         0.30         4.31         8.94         3.35 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW 
       19.50         4.08         3.32         7.17        30.74         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-LN-A49K 
        6.94         2.60        25.12         7.40        16.47         0.07 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.10         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-RE-A7BO 
       17.62         5.16         7.59         7.04        29.59         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW 
        8.78        14.01 

$`DEL PEAK  6(3P25.3) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.03         0.99         0.36         1.12         0.46       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       44.75         3.68        41.52        42.77         6.21         3.16 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
        3.52         3.68         8.78         6.41        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Y 
        3.16         4.90        29.00         7.43         8.71         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49M 
        3.95         3.02        21.37        83.24        10.36         0.16 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.10         0.07         0.07         3.78         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-V5-A7RB TCGA-V5-A7RE 
       14.70         6.35        53.95         9.30         5.29         4.80 

  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                        60.39                        122.10 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                         3.40                          4.98 
[1] "0.1 - 60.4 (3.4)"  "0.0 - 122.1 (5.0)"
[1] "hr=" "1.4"
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(3P25.3) MUTATED         4        2        3        1        21
  DEL PEAK  6(3P25.3) WILD-TYPE       3        2        1        0         9
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P25.3) MUTATED           9         7          6          2
  DEL PEAK  6(3P25.3) WILD-TYPE         7         4          2          4
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  6(3P25.3) MUTATED            1        0
  DEL PEAK  6(3P25.3) WILD-TYPE          2        1
D32V3, multiclass
            clus
vv           DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  STAGE I                              4                             3
  STAGE IA                             2                             2
  STAGE IB                             3                             1
  STAGE II                             1                             0
  STAGE IIA                           21                             9
  STAGE IIB                            9                             7
  STAGE III                            7                             4
  STAGE IIIA                           6                             2
  STAGE IIIB                           2                             4
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK  6(3P25.3) MUTATED       9 16    32
  DEL PEAK  6(3P25.3) WILD-TYPE    10 10    18
D32V4, multiclass
       clus
vv      DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  T0+T1                           9                            10
  T2                             16                            10
  T3+T4                          32                            18
[1] 3 2
[1] 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(3P25.3) MUTATED   34 19     4
  DEL PEAK  6(3P25.3) WILD-TYPE 16 14     7
D32V5, multiclass
       clus
vv      DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  N0                             34                            16
  N1                             19                            14
  N2+N3                           4                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK  6(3P25.3) MUTATED   48   0  8
  DEL PEAK  6(3P25.3) WILD-TYPE 27   1  7
D32V6, multiclass
     clus
vv    DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  M0                           48                            27
  M1A                           0                             1
  MX                            8                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P25.3) MUTATED   12 48
  DEL PEAK  6(3P25.3) WILD-TYPE  3 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED     12   48
  DEL PEAK  6(3P25.3) WILD-TYPE    3   42
        clus
vv       DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  FEMALE                          12                             3
  MALE                            48                            42
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P25.3) MUTATED   25 32
  DEL PEAK  6(3P25.3) WILD-TYPE 10 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED     25   32
  DEL PEAK  6(3P25.3) WILD-TYPE   10   34
       clus
vv      DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  ASIAN                          25                            10
  WHITE                          32                            34
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  7(3P14.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(3P14.3) MUTATED   47 17
  DEL PEAK  7(3P14.3) WILD-TYPE 20 14
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           64                            34 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           17                            14 
$`DEL PEAK  7(3P14.3) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.03         0.26         0.53        17.03         0.79         0.13 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       44.75        60.39        53.85         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        8.94         3.68         3.35        19.50         6.41         4.08 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.32         7.17         1.38         7.13         7.43         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49K 
        2.60         0.36         7.40        16.47        83.24         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.10         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6L6 
        0.20         1.18        17.62         5.16         7.59         7.04 
TCGA-R6-A6XG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59         7.00         8.78        14.01 

$`DEL PEAK  7(3P14.3) WILD-TYPE`
TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE 
        0.99         0.36         1.12         0.46       122.10         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OI 
       41.52        42.77         6.21         3.16         3.52         8.78 
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T 
       18.35         3.16        30.74         4.90        29.00         8.71 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49V 
       25.12         3.95         3.02        21.37        10.36         0.10 
TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ 
        0.07         3.78         8.02         5.06        14.70         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30         5.29         4.80 

  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                         0.03                          0.07 
  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 
                        3.335                         5.750 
[1] "0.0 - 83.2 (3.3)"  "0.1 - 122.1 (5.8)"
[1] "hr=" "1.1"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3P14.3) MUTATED         5        2        3        1        24
  DEL PEAK  7(3P14.3) WILD-TYPE       2        2        1        0         6
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P14.3) MUTATED          12         9          7          2
  DEL PEAK  7(3P14.3) WILD-TYPE         4         2          1          4
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  7(3P14.3) MUTATED            1        0
  DEL PEAK  7(3P14.3) WILD-TYPE          2        1
D33V3, multiclass
            clus
vv           DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  STAGE I                              5                             2
  STAGE IA                             2                             2
  STAGE IB                             3                             1
  STAGE II                             1                             0
  STAGE IIA                           24                             6
  STAGE IIB                           12                             4
  STAGE III                            9                             2
  STAGE IIIA                           7                             1
  STAGE IIIB                           2                             4
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK  7(3P14.3) MUTATED      12 21    35
  DEL PEAK  7(3P14.3) WILD-TYPE     7  5    15
D33V4, multiclass
       clus
vv      DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  T0+T1                          12                             7
  T2                             21                             5
  T3+T4                          35                            15
[1] 3 2
[1] 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   39 24     5
  DEL PEAK  7(3P14.3) WILD-TYPE 11  9     6
D33V5, multiclass
       clus
vv      DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  N0                             39                            11
  N1                             24                             9
  N2+N3                           5                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK  7(3P14.3) MUTATED   57   0  9
  DEL PEAK  7(3P14.3) WILD-TYPE 18   1  6
D33V6, multiclass
     clus
vv    DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  M0                           57                            18
  M1A                           0                             1
  MX                            9                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED   12 59
  DEL PEAK  7(3P14.3) WILD-TYPE  3 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED     12   59
  DEL PEAK  7(3P14.3) WILD-TYPE    3   31
        clus
vv       DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  FEMALE                          12                             3
  MALE                            59                            31
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED   31 37
  DEL PEAK  7(3P14.3) WILD-TYPE  4 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED     31   37
  DEL PEAK  7(3P14.3) WILD-TYPE    4   29
       clus
vv      DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  ASIAN                          31                             4
  WHITE                          37                            29
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  8(3P14.2) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(3P14.2) MUTATED   46 17
  DEL PEAK  8(3P14.2) WILD-TYPE 21 14
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           63                            35 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           17                            14 
$`DEL PEAK  8(3P14.2) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.03         0.26         0.53        17.03         0.79         0.13 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       44.75        53.85         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.52         3.68         3.35        19.50         6.41         4.08 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.32         7.17         1.38         7.13         7.43         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-LN-A49K TCGA-LN-A49L 
        2.60         0.36         7.40        16.47         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        0.16         0.07         0.33         0.13         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.10         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO 
       17.62         5.16         8.02         7.59         7.04         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE 
        8.78        14.01         4.80 

$`DEL PEAK  8(3P14.2) WILD-TYPE`
TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB 
        0.99         0.36         1.12         0.46       122.10        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OI 
        3.68        41.52        42.77         6.21         3.16         8.78 
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T 
       18.35         3.16        30.74         4.90        29.00         8.71 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
       25.12         3.95         3.02        21.37        83.24        10.36 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.10         0.10         0.07         3.78         5.06        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-V5-A7RB 
       29.59         6.35        53.95         9.30         5.29 

  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                        53.85                        122.10 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         3.35                          6.35 
[1] "0.0 - 53.9 (3.4)"  "0.1 - 122.1 (6.3)"
[1] "hr=" "1.3"
D34V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P14.2) MUTATED         4        2        4        1        23
  DEL PEAK  8(3P14.2) WILD-TYPE       3        2        0        0         7
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P14.2) MUTATED          12         8          7          3
  DEL PEAK  8(3P14.2) WILD-TYPE         4         3          1          3
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  8(3P14.2) MUTATED            1        0
  DEL PEAK  8(3P14.2) WILD-TYPE          2        1
D34V3, multiclass
            clus
vv           DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  STAGE I                              4                             3
  STAGE IA                             2                             2
  STAGE IB                             4                             0
  STAGE II                             1                             0
  STAGE IIA                           23                             7
  STAGE IIB                           12                             4
  STAGE III                            8                             3
  STAGE IIIA                           7                             1
  STAGE IIIB                           3                             3
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK  8(3P14.2) MUTATED      12 20    35
  DEL PEAK  8(3P14.2) WILD-TYPE     7  6    15
D34V4, multiclass
       clus
vv      DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T0+T1                          12                             7
  T2                             20                             6
  T3+T4                          35                            15
[1] 3 2
[1] 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   38 23     6
  DEL PEAK  8(3P14.2) WILD-TYPE 12 10     5
D34V5, multiclass
       clus
vv      DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                             38                            12
  N1                             23                            10
  N2+N3                           6                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK  8(3P14.2) MUTATED   55   0  9
  DEL PEAK  8(3P14.2) WILD-TYPE 20   1  6
D34V6, multiclass
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  M0                           55                            20
  M1A                           0                             1
  MX                            9                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED   12 58
  DEL PEAK  8(3P14.2) WILD-TYPE  3 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     12   58
  DEL PEAK  8(3P14.2) WILD-TYPE    3   32
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                          12                             3
  MALE                            58                            32
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED   30 37
  DEL PEAK  8(3P14.2) WILD-TYPE  5 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     30   37
  DEL PEAK  8(3P14.2) WILD-TYPE    5   29
       clus
vv      DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  ASIAN                          30                             5
  WHITE                          37                            29
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  9(3Q11.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(3Q11.1) MUTATED    9  3
  DEL PEAK  9(3Q11.1) WILD-TYPE 58 28
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           12                            86 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                            3                            28 
$`DEL PEAK  9(3Q11.1) MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OX 
        2.63        20.12        53.85         3.45        19.50         7.43 
TCGA-L5-A88Y TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-RE-A7BO 
        0.36        10.45         0.07         0.10         0.20         7.00 

$`DEL PEAK  9(3Q11.1) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27        20.09         0.85        20.78         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.99         0.53        17.03         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
        1.12         0.46       122.10        44.75        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
       41.52        42.77         6.21         3.16         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94         3.52         3.68         3.35         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.08        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T 
       30.74         4.90        29.00         7.13         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        2.60        25.12         7.40         3.95         3.02        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       21.37        83.24        10.36         0.07         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        0.33         0.10         0.13         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.10         0.07         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        3.78         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59         6.35        53.95         9.30         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                        53.85                        122.10 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                        5.225                         4.195 
[1] "0.1 - 53.9 (5.2)"  "0.0 - 122.1 (4.2)"
[1] "hr=" "1.3"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3Q11.1) MUTATED         2        0        0        1         4
  DEL PEAK  9(3Q11.1) WILD-TYPE       5        4        4        0        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3Q11.1) MUTATED           3         1          2          0
  DEL PEAK  9(3Q11.1) WILD-TYPE        13        10          6          6
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  9(3Q11.1) MUTATED            0        0
  DEL PEAK  9(3Q11.1) WILD-TYPE          3        1
D35V3, multiclass
            clus
vv           DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  STAGE I                              2                             5
  STAGE IA                             0                             4
  STAGE IB                             0                             4
  STAGE II                             1                             0
  STAGE IIA                            4                            26
  STAGE IIB                            3                            13
  STAGE III                            1                            10
  STAGE IIIA                           2                             6
  STAGE IIIB                           0                             6
  STAGE IIIC                           0                             3
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK  9(3Q11.1) MUTATED       4  5     5
  DEL PEAK  9(3Q11.1) WILD-TYPE    15 21    45
D35V4, multiclass
       clus
vv      DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  T0+T1                           4                            15
  T2                              5                            21
  T3+T4                           5                            45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  9(3Q11.1) MUTATED    8  6     0
  DEL PEAK  9(3Q11.1) WILD-TYPE 42 27    11
D35V5, multiclass
       clus
vv      DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  N0                              8                            42
  N1                              6                            27
  N2+N3                           0                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK  9(3Q11.1) MUTATED   13   0  1
  DEL PEAK  9(3Q11.1) WILD-TYPE 62   1 14
D35V6, multiclass
     clus
vv    DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  M0                           13                            62
  M1A                           0                             1
  MX                            1                            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                             0  1
  DEL PEAK  9(3Q11.1) MUTATED    2 12
  DEL PEAK  9(3Q11.1) WILD-TYPE 13 78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED      2   12
  DEL PEAK  9(3Q11.1) WILD-TYPE   13   78
        clus
vv       DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  FEMALE                           2                            13
  MALE                            12                            78
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, binary
                               cls
clus                             0  1
  DEL PEAK  9(3Q11.1) MUTATED    7  7
  DEL PEAK  9(3Q11.1) WILD-TYPE 28 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED      7    7
  DEL PEAK  9(3Q11.1) WILD-TYPE   28   59
       clus
vv      DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  ASIAN                           7                            28
  WHITE                           7                            59
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 10(3Q26.31) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(3Q26.31) MUTATED    3  5
  DEL PEAK 10(3Q26.31) WILD-TYPE 64 26
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             8                             90 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             5                             26 
$`DEL PEAK 10(3Q26.31) MUTATED`
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A891 TCGA-LN-A4MR 
       19.50        18.35         1.38         7.43         3.95         0.07 
TCGA-R6-A6DN TCGA-RE-A7BO 
        8.02         7.00 

$`DEL PEAK 10(3Q26.31) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        0.03         0.26         0.99         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.36         0.13         1.12         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
       60.39        53.85         3.68        41.52        42.77         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        3.16         3.45         0.30         4.31         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
        3.68         3.35         8.78         6.41         4.08         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K 
        3.02        16.47        21.37        83.24        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.07         0.10         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.20         1.18        17.62         5.16         3.78 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30         8.78        14.01         5.29         4.80 

  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          19.5                          122.1 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                         7.215                          3.930 
[1] "0.1 - 19.5 (7.2)"  "0.0 - 122.1 (3.9)"
[1] "hr=" "2.1"
D36V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3Q26.31) MUTATED         1        0        0        0         1
  DEL PEAK 10(3Q26.31) WILD-TYPE       6        4        4        1        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3Q26.31) MUTATED           3         0          1          0
  DEL PEAK 10(3Q26.31) WILD-TYPE        13        11          7          6
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 10(3Q26.31) MUTATED            0        0
  DEL PEAK 10(3Q26.31) WILD-TYPE          3        1
D36V3, multiclass
            clus
vv           DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  STAGE I                               1                              6
  STAGE IA                              0                              4
  STAGE IB                              0                              4
  STAGE II                              0                              1
  STAGE IIA                             1                             29
  STAGE IIB                             3                             13
  STAGE III                             0                             11
  STAGE IIIA                            1                              7
  STAGE IIIB                            0                              6
  STAGE IIIC                            0                              3
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 10(3Q26.31) MUTATED       3  3     1
  DEL PEAK 10(3Q26.31) WILD-TYPE    16 23    49
D36V4, multiclass
       clus
vv      DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  T0+T1                            3                             16
  T2                               3                             23
  T3+T4                            1                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 10(3Q26.31) MUTATED    2  4     1
  DEL PEAK 10(3Q26.31) WILD-TYPE 48 29    10
D36V5, multiclass
       clus
vv      DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  N0                               2                             48
  N1                               4                             29
  N2+N3                            1                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 10(3Q26.31) MUTATED    5   0  1
  DEL PEAK 10(3Q26.31) WILD-TYPE 70   1 14
D36V6, multiclass
     clus
vv    DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  M0                             5                             70
  M1A                            0                              1
  MX                             1                             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                                cls
clus                              0  1
  DEL PEAK 10(3Q26.31) MUTATED    1  7
  DEL PEAK 10(3Q26.31) WILD-TYPE 14 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      1    7
  DEL PEAK 10(3Q26.31) WILD-TYPE   14   83
        clus
vv       DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  FEMALE                            1                             14
  MALE                              7                             83
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, binary
                                cls
clus                              0  1
  DEL PEAK 10(3Q26.31) MUTATED    1  7
  DEL PEAK 10(3Q26.31) WILD-TYPE 34 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      1    7
  DEL PEAK 10(3Q26.31) WILD-TYPE   34   59
       clus
vv      DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  ASIAN                            1                             34
  WHITE                            7                             59
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 11(4P15.2) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(4P15.2) MUTATED   35 19
  DEL PEAK 11(4P15.2) WILD-TYPE 32 12
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           54                            44 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           19                            12 
$`DEL PEAK 11(4P15.2) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.26         0.53         0.79         0.36         0.13         0.46 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE 
       44.75        60.39        42.77         3.16         8.94         3.52 
TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT 
        3.35         6.41         4.08         3.32         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L7-A6VZ 
        7.13         7.43         7.40         3.95        16.47        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U 
        0.07        10.45         0.16         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.10         0.07         0.13         0.07         0.10         0.07 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.20         1.18         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
        7.04         6.35         9.30         7.00        14.01         4.80 

$`DEL PEAK 11(4P15.2) WILD-TYPE`
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD 
        2.63         0.99        17.03         1.12       122.10        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52         6.21         3.45         0.30         4.31 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        3.68        19.50         8.78        18.35         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       30.74        29.00         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49O TCGA-LN-A49S 
        0.36         3.02        21.37        83.24         0.33         0.13 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.07         0.10         0.10         0.07         0.10 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 
       17.62         5.16         3.78        14.70        29.59        53.95 
TCGA-S8-A6BV TCGA-V5-A7RB 
        8.78         5.29 

  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                         0.03                          0.07 
  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 
                        3.735                         5.225 
[1] "0.0 - 60.4 (3.7)"  "0.1 - 122.1 (5.2)"
[1] "hr=" "2"  
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4P15.2) MUTATED         3        2        3        1        16
  DEL PEAK 11(4P15.2) WILD-TYPE       4        2        1        0        14
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4P15.2) MUTATED          10         3          4          4
  DEL PEAK 11(4P15.2) WILD-TYPE         6         8          4          2
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 11(4P15.2) MUTATED            2        1
  DEL PEAK 11(4P15.2) WILD-TYPE          1        0
D37V3, multiclass
            clus
vv           DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  STAGE I                              3                             4
  STAGE IA                             2                             2
  STAGE IB                             3                             1
  STAGE II                             1                             0
  STAGE IIA                           16                            14
  STAGE IIB                           10                             6
  STAGE III                            3                             8
  STAGE IIIA                           4                             4
  STAGE IIIB                           4                             2
  STAGE IIIC                           2                             1
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 11(4P15.2) MUTATED       8 18    25
  DEL PEAK 11(4P15.2) WILD-TYPE    11  8    25
D37V4, multiclass
       clus
vv      DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T0+T1                           8                            11
  T2                             18                             8
  T3+T4                          25                            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 11(4P15.2) MUTATED   27 17     7
  DEL PEAK 11(4P15.2) WILD-TYPE 23 16     4
D37V5, multiclass
       clus
vv      DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                             27                            23
  N1                             17                            16
  N2+N3                           7                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 11(4P15.2) MUTATED   44   1  4
  DEL PEAK 11(4P15.2) WILD-TYPE 31   0 11
D37V6, multiclass
     clus
vv    DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  M0                           44                            31
  M1A                           1                             0
  MX                            4                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED    9 49
  DEL PEAK 11(4P15.2) WILD-TYPE  6 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED      9   49
  DEL PEAK 11(4P15.2) WILD-TYPE    6   41
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                           9                             6
  MALE                            49                            41
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED   23 33
  DEL PEAK 11(4P15.2) WILD-TYPE 12 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     23   33
  DEL PEAK 11(4P15.2) WILD-TYPE   12   33
       clus
vv      DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  ASIAN                          23                            12
  WHITE                          33                            33
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 12(4Q21.23) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(4Q21.23) MUTATED   32 19
  DEL PEAK 12(4Q21.23) WILD-TYPE 35 12
  DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE 
                            51                             47 
  DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE 
                            19                             12 
$`DEL PEAK 12(4Q21.23) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       33.27        20.09         0.85         0.26         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43J 
        0.36         0.46        60.39        42.77         3.16         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        8.94         3.52         3.35         3.16        30.74         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43         6.94         2.60         7.40         3.95 
TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       16.47        83.24        10.36         0.07        10.45         0.16 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 
        0.33         0.10         0.07         0.07         0.07         0.07 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.10         0.10         0.20         1.18         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        5.06         7.04        29.59         6.35         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE 
        8.78        14.01         4.80 

$`DEL PEAK 12(4Q21.23) WILD-TYPE`
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       20.78         2.63        20.12         0.03         0.99        17.03 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        0.13         1.12       122.10        44.75        53.85         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       41.52         6.21         3.45         0.30         3.68        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        8.78         6.41         4.08        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 
        1.38        29.00         8.71        25.12         0.36         3.02 
TCGA-L5-A8NQ TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 
       21.37         0.07         0.13         0.10         0.10         0.13 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-M9-A5M8 
        0.10         0.10         0.07         0.07         0.07        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-V5-A7RB 
        5.16         3.78        14.70        53.95         5.29 

  DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE 
                          4.80                           3.78 
[1] "0.1 - 83.2 (4.8)"  "0.0 - 122.1 (3.8)"
[1] "hr=" "1.6"
D38V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(4Q21.23) MUTATED         2        1        4        1        14
  DEL PEAK 12(4Q21.23) WILD-TYPE       5        3        0        0        16
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q21.23) MUTATED           8         6          3          4
  DEL PEAK 12(4Q21.23) WILD-TYPE         8         5          5          2
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 12(4Q21.23) MUTATED            1        1
  DEL PEAK 12(4Q21.23) WILD-TYPE          2        0
D38V3, multiclass
            clus
vv           DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE
  STAGE I                               2                              5
  STAGE IA                              1                              3
  STAGE IB                              4                              0
  STAGE II                              1                              0
  STAGE IIA                            14                             16
  STAGE IIB                             8                              8
  STAGE III                             6                              5
  STAGE IIIA                            3                              5
  STAGE IIIB                            4                              2
  STAGE IIIC                            1                              2
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 12(4Q21.23) MUTATED       6 14    27
  DEL PEAK 12(4Q21.23) WILD-TYPE    13 12    23
D38V4, multiclass
       clus
vv      DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE
  T0+T1                            6                             13
  T2                              14                             12
  T3+T4                           27                             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 12(4Q21.23) MUTATED   24 17     6
  DEL PEAK 12(4Q21.23) WILD-TYPE 26 16     5
D38V5, multiclass
       clus
vv      DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE
  N0                              24                             26
  N1                              17                             16
  N2+N3                            6                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 12(4Q21.23) MUTATED   37   1  8
  DEL PEAK 12(4Q21.23) WILD-TYPE 38   0  7
D38V6, multiclass
     clus
vv    DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE
  M0                            37                             38
  M1A                            1                              0
  MX                             8                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                                cls
clus                              0  1
  DEL PEAK 12(4Q21.23) MUTATED    8 47
  DEL PEAK 12(4Q21.23) WILD-TYPE  7 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(4Q21.23) MUTATED      8   47
  DEL PEAK 12(4Q21.23) WILD-TYPE    7   43
        clus
vv       DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE
  FEMALE                            8                              7
  MALE                             47                             43
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, binary
                                cls
clus                              0  1
  DEL PEAK 12(4Q21.23) MUTATED   20 33
  DEL PEAK 12(4Q21.23) WILD-TYPE 15 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(4Q21.23) MUTATED     20   33
  DEL PEAK 12(4Q21.23) WILD-TYPE   15   33
       clus
vv      DEL PEAK 12(4Q21.23) MUTATED DEL PEAK 12(4Q21.23) WILD-TYPE
  ASIAN                           20                             15
  WHITE                           33                             33
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 13(4Q22.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(4Q22.1) MUTATED   33 21
  DEL PEAK 13(4Q22.1) WILD-TYPE 34 10
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                           54                            44 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                           21                            10 
$`DEL PEAK 13(4Q22.1) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       33.27        20.09         0.85         0.26         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-L5-A43C 
        0.36         0.46        44.75        60.39        42.77         3.16 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OQ 
        4.31         8.94         3.52         3.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        30.74         4.90         7.13         7.43         6.94 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L7-A6VZ 
        2.60         7.40         3.95        16.47        83.24        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
        0.07        10.45         0.16         0.33         0.10         0.07 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 
        0.07         0.07         0.07         0.10         0.10         0.20 
TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        1.18         8.02         7.59         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE 
        6.35         9.30         7.00         8.78        14.01         4.80 

$`DEL PEAK 13(4Q22.1) WILD-TYPE`
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       20.78         2.63        20.12         0.03         0.99        17.03 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.13         1.12       122.10        53.85         3.68        41.52 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        6.21         3.45         0.30         3.68        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A88T 
        6.41         4.08        18.35         7.17        29.00         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NQ TCGA-LN-A49N TCGA-LN-A49S 
       25.12         0.36         3.02        21.37         0.07         0.13 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.10         0.13         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 
        0.07         0.07        17.62         5.16         3.78        14.70 
TCGA-R6-A6Y0 TCGA-V5-A7RB 
       53.95         5.29 

  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                        4.555                         3.930 
[1] "0.1 - 83.2 (4.6)"  "0.0 - 122.1 (3.9)"
[1] "hr=" "1.8"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4Q22.1) MUTATED         2        1        4        1        14
  DEL PEAK 13(4Q22.1) WILD-TYPE       5        3        0        0        16
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4Q22.1) MUTATED           9         6          4          4
  DEL PEAK 13(4Q22.1) WILD-TYPE         7         5          4          2
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 13(4Q22.1) MUTATED            2        1
  DEL PEAK 13(4Q22.1) WILD-TYPE          1        0
D39V3, multiclass
            clus
vv           DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  STAGE I                              2                             5
  STAGE IA                             1                             3
  STAGE IB                             4                             0
  STAGE II                             1                             0
  STAGE IIA                           14                            16
  STAGE IIB                            9                             7
  STAGE III                            6                             5
  STAGE IIIA                           4                             4
  STAGE IIIB                           4                             2
  STAGE IIIC                           2                             1
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 13(4Q22.1) MUTATED       6 16    28
  DEL PEAK 13(4Q22.1) WILD-TYPE    13 10    22
D39V4, multiclass
       clus
vv      DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  T0+T1                           6                            13
  T2                             16                            10
  T3+T4                          28                            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 13(4Q22.1) MUTATED   24 18     8
  DEL PEAK 13(4Q22.1) WILD-TYPE 26 15     3
D39V5, multiclass
       clus
vv      DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  N0                             24                            26
  N1                             18                            15
  N2+N3                           8                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 13(4Q22.1) MUTATED   39   1  9
  DEL PEAK 13(4Q22.1) WILD-TYPE 36   0  6
D39V6, multiclass
     clus
vv    DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  M0                           39                            36
  M1A                           1                             0
  MX                            9                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q22.1) MUTATED    8 50
  DEL PEAK 13(4Q22.1) WILD-TYPE  7 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q22.1) MUTATED      8   50
  DEL PEAK 13(4Q22.1) WILD-TYPE    7   40
        clus
vv       DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  FEMALE                           8                             7
  MALE                            50                            40
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q22.1) MUTATED   21 35
  DEL PEAK 13(4Q22.1) WILD-TYPE 14 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q22.1) MUTATED     21   35
  DEL PEAK 13(4Q22.1) WILD-TYPE   14   31
       clus
vv      DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  ASIAN                          21                            14
  WHITE                          35                            31
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 14(4Q31.3) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(4Q31.3) MUTATED   30 21
  DEL PEAK 14(4Q31.3) WILD-TYPE 37 10
  DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE 
                           51                            47 
  DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE 
                           21                            10 
$`DEL PEAK 14(4Q31.3) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       33.27        20.09         0.85         0.26         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-L5-A43C 
        0.36         0.46        44.75        60.39        42.77         3.16 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OS 
        4.31         8.94         3.52         3.35         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A88Z 
        4.90         7.13         7.43         6.94         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        3.95        16.47        83.24        10.36         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
        0.16         0.10         0.07         0.07         0.10         0.10 
TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.20         5.16         3.78         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.04        29.59         6.35        53.95         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE 
        8.78        14.01         4.80 

$`DEL PEAK 14(4Q31.3) WILD-TYPE`
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       20.78         2.63        20.12         0.03         0.99        17.03 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.13         1.12       122.10        53.85         3.68        41.52 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        6.21         3.45         0.30         3.68        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        6.41         4.08        18.35         3.32         7.17         1.38 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NQ 
       29.00         8.71         2.60        25.12         3.02        21.37 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
        0.07         0.33         0.13         0.07         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.13         0.10         0.10         0.07         0.07 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-R6-A6L4 TCGA-V5-A7RB 
        0.07         1.18        17.62        14.70         5.29 

  DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE 
                         5.16                          3.32 
[1] "0.1 - 83.2 (5.2)"  "0.0 - 122.1 (3.3)"
[1] "hr=" "1.6"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(4Q31.3) MUTATED         2        1        4        1        11
  DEL PEAK 14(4Q31.3) WILD-TYPE       5        3        0        0        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(4Q31.3) MUTATED           9         5          3          6
  DEL PEAK 14(4Q31.3) WILD-TYPE         7         6          5          0
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 14(4Q31.3) MUTATED            1        1
  DEL PEAK 14(4Q31.3) WILD-TYPE          2        0
D40V3, multiclass
            clus
vv           DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE
  STAGE I                              2                             5
  STAGE IA                             1                             3
  STAGE IB                             4                             0
  STAGE II                             1                             0
  STAGE IIA                           11                            19
  STAGE IIB                            9                             7
  STAGE III                            5                             6
  STAGE IIIA                           3                             5
  STAGE IIIB                           6                             0
  STAGE IIIC                           1                             2
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 14(4Q31.3) MUTATED       7 15    25
  DEL PEAK 14(4Q31.3) WILD-TYPE    12 11    25
D40V4, multiclass
       clus
vv      DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE
  T0+T1                           7                            12
  T2                             15                            11
  T3+T4                          25                            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 14(4Q31.3) MUTATED   22 17     8
  DEL PEAK 14(4Q31.3) WILD-TYPE 28 16     3
D40V5, multiclass
       clus
vv      DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE
  N0                             22                            28
  N1                             17                            16
  N2+N3                           8                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 14(4Q31.3) MUTATED   37   1  8
  DEL PEAK 14(4Q31.3) WILD-TYPE 38   0  7
D40V6, multiclass
     clus
vv    DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE
  M0                           37                            38
  M1A                           1                             0
  MX                            8                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                               cls
clus                             0  1
  DEL PEAK 14(4Q31.3) MUTATED    9 47
  DEL PEAK 14(4Q31.3) WILD-TYPE  6 43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q31.3) MUTATED      9   47
  DEL PEAK 14(4Q31.3) WILD-TYPE    6   43
        clus
vv       DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE
  FEMALE                           9                             6
  MALE                            47                            43
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, binary
                               cls
clus                             0  1
  DEL PEAK 14(4Q31.3) MUTATED   18 36
  DEL PEAK 14(4Q31.3) WILD-TYPE 17 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q31.3) MUTATED     18   36
  DEL PEAK 14(4Q31.3) WILD-TYPE   17   30
       clus
vv      DEL PEAK 14(4Q31.3) MUTATED DEL PEAK 14(4Q31.3) WILD-TYPE
  ASIAN                          18                            17
  WHITE                          36                            30
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 15(5Q11.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(5Q11.2) MUTATED   41 14
  DEL PEAK 15(5Q11.2) WILD-TYPE 26 17
  DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE 
                           55                            43 
  DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE 
                           14                            17 
$`DEL PEAK 15(5Q11.2) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L 
       33.27        20.09         0.85         2.63         0.26         0.53 
TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH 
       17.03         0.46       122.10        44.75        60.39        42.77 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        3.45         4.31         3.52         3.68         3.35        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
        6.41         4.08         3.32         7.17         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        4.90         7.13         2.60         0.36         3.95         3.02 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R 
       21.37        10.36         0.07        10.45         0.07         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
        0.13         0.07         0.10         0.07         0.07         0.13 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.10         0.07         0.10         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.16         5.06        29.59         6.35        53.95         9.30 
TCGA-S8-A6BV 
        8.78 

$`DEL PEAK 15(5Q11.2) WILD-TYPE`
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 
       20.78        20.12         0.03         0.99         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
        0.13         1.12        53.85         3.68        41.52         6.21 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OQ 
        3.16         0.30         8.94         8.78        18.35         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49X TCGA-LN-A4A3 
       16.47        83.24         0.16         0.33         0.10         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.10         0.10         0.07         0.07         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        7.59        14.70         7.04         7.00        14.01         5.29 
TCGA-V5-A7RE 
        4.80 

  DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE 
                       122.10                         83.24 
  DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE 
                         3.68                          6.21 
[1] "0.1 - 122.1 (3.7)" "0.0 - 83.2 (6.2)" 
[1] "hr=" "1.5"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(5Q11.2) MUTATED         7        3        0        0        17
  DEL PEAK 15(5Q11.2) WILD-TYPE       0        1        4        1        13
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q11.2) MUTATED          10         5          4          4
  DEL PEAK 15(5Q11.2) WILD-TYPE         6         6          4          2
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 15(5Q11.2) MUTATED            2        1
  DEL PEAK 15(5Q11.2) WILD-TYPE          1        0
D41V3, multiclass
            clus
vv           DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE
  STAGE I                              7                             0
  STAGE IA                             3                             1
  STAGE IB                             0                             4
  STAGE II                             0                             1
  STAGE IIA                           17                            13
  STAGE IIB                           10                             6
  STAGE III                            5                             6
  STAGE IIIA                           4                             4
  STAGE IIIB                           4                             2
  STAGE IIIC                           2                             1
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 15(5Q11.2) MUTATED      13 15    27
  DEL PEAK 15(5Q11.2) WILD-TYPE     6 11    23
D41V4, multiclass
       clus
vv      DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE
  T0+T1                          13                             6
  T2                             15                            11
  T3+T4                          27                            23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 15(5Q11.2) MUTATED   31 18     6
  DEL PEAK 15(5Q11.2) WILD-TYPE 19 15     5
D41V5, multiclass
       clus
vv      DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE
  N0                             31                            19
  N1                             18                            15
  N2+N3                           6                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 15(5Q11.2) MUTATED   44   1  7
  DEL PEAK 15(5Q11.2) WILD-TYPE 31   0  8
D41V6, multiclass
     clus
vv    DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE
  M0                           44                            31
  M1A                           1                             0
  MX                            7                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                               cls
clus                             0  1
  DEL PEAK 15(5Q11.2) MUTATED    9 51
  DEL PEAK 15(5Q11.2) WILD-TYPE  6 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q11.2) MUTATED      9   51
  DEL PEAK 15(5Q11.2) WILD-TYPE    6   39
        clus
vv       DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE
  FEMALE                           9                             6
  MALE                            51                            39
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, binary
                               cls
clus                             0  1
  DEL PEAK 15(5Q11.2) MUTATED   23 35
  DEL PEAK 15(5Q11.2) WILD-TYPE 12 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q11.2) MUTATED     23   35
  DEL PEAK 15(5Q11.2) WILD-TYPE   12   31
       clus
vv      DEL PEAK 15(5Q11.2) MUTATED DEL PEAK 15(5Q11.2) WILD-TYPE
  ASIAN                          23                            12
  WHITE                          35                            31
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 16(5Q15) MUTATION ANALYSIS
D42V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 16(5Q15) MUTATED   43 12
  DEL PEAK 16(5Q15) WILD-TYPE 24 19
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                         55                          43 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                         12                          19 
$`DEL PEAK 16(5Q15) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27        20.09         2.63        20.12         0.03         0.26 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
        0.53        17.03         0.46       122.10        60.39        42.77 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        3.45         4.31         3.52         3.68         3.35        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
        6.41         4.08         3.32         7.17         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        4.90         7.13         2.60         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        3.02        21.37         0.07        10.45         0.16         0.07 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 
        0.10         0.13         0.07         0.10         0.07         0.13 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-M9-A5M8 
        0.10         0.10         0.07         0.10         0.20        17.62 
TCGA-Q9-A6FU TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV 
        5.16        29.59         6.35        53.95         9.30         8.78 
TCGA-S8-A6BW 
       14.01 

$`DEL PEAK 16(5Q15) WILD-TYPE`
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.85        20.78         0.99         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
        1.12        44.75        53.85         3.68        41.52         6.21 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OQ 
        3.16         0.30         8.94         8.78        18.35         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NJ 
       29.00         7.43         6.94         8.71        25.12        16.47 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
       83.24        10.36         0.33         0.10         0.07         0.07 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.10         0.07         0.07         1.18         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-V5-A7RB 
        7.59         5.06        14.70         7.04         7.00         5.29 
TCGA-V5-A7RE 
        4.80 

  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                       0.03                        0.07 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                     122.10                       83.24 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                       3.68                        5.29 
[1] "0.0 - 122.1 (3.7)" "0.1 - 83.2 (5.3)" 
[1] "hr=" "1.8"
D42V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(5Q15) MUTATED         7        3        1        0        17
  DEL PEAK 16(5Q15) WILD-TYPE       0        1        3        1        13
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(5Q15) MUTATED          10         6          4          4
  DEL PEAK 16(5Q15) WILD-TYPE         6         5          4          2
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 16(5Q15) MUTATED            1        1
  DEL PEAK 16(5Q15) WILD-TYPE          2        0
D42V3, multiclass
            clus
vv           DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  STAGE I                            7                           0
  STAGE IA                           3                           1
  STAGE IB                           1                           3
  STAGE II                           0                           1
  STAGE IIA                         17                          13
  STAGE IIB                         10                           6
  STAGE III                          6                           5
  STAGE IIIA                         4                           4
  STAGE IIIB                         4                           2
  STAGE IIIC                         1                           2
  STAGE IV                           1                           0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3+T4
  DEL PEAK 16(5Q15) MUTATED      14 16    26
  DEL PEAK 16(5Q15) WILD-TYPE     5 10    24
D42V4, multiclass
       clus
vv      DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  T0+T1                        14                           5
  T2                           16                          10
  T3+T4                        26                          24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2+N3
  DEL PEAK 16(5Q15) MUTATED   30 21     5
  DEL PEAK 16(5Q15) WILD-TYPE 20 12     6
D42V5, multiclass
       clus
vv      DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  N0                           30                          20
  N1                           21                          12
  N2+N3                         5                           6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1A MX
  DEL PEAK 16(5Q15) MUTATED   45   1  7
  DEL PEAK 16(5Q15) WILD-TYPE 30   0  8
D42V6, multiclass
     clus
vv    DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  M0                         45                          30
  M1A                         1                           0
  MX                          7                           8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                             cls
clus                           0  1
  DEL PEAK 16(5Q15) MUTATED   10 50
  DEL PEAK 16(5Q15) WILD-TYPE  5 40
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(5Q15) MUTATED     10   50
  DEL PEAK 16(5Q15) WILD-TYPE    5   40
        clus
vv       DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  FEMALE                        10                           5
  MALE                          50                          40
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, binary
                             cls
clus                           0  1
  DEL PEAK 16(5Q15) MUTATED   22 36
  DEL PEAK 16(5Q15) WILD-TYPE 13 30
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(5Q15) MUTATED     22   36
  DEL PEAK 16(5Q15) WILD-TYPE   13   30
       clus
vv      DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  ASIAN                        22                          13
  WHITE                        36                          30
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 17(6P25.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 17(6P25.3) MUTATED   22 13
  DEL PEAK 17(6P25.3) WILD-TYPE 45 18
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                           35                            63 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                           13                            18 
$`DEL PEAK 17(6P25.3) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-JY-A6F8 TCGA-JY-A6FB 
       33.27         0.03         0.26         0.53       122.10        60.39 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4ON 
        3.16         3.45         0.30         4.31         3.35        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88Y 
        3.32         7.17         1.38         3.16         7.13         0.36 
TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A49W 
       16.47        10.36         0.07         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ 
        0.13         0.20         1.18        17.62         5.16         7.59 
TCGA-R6-A6L4 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       14.70         9.30         8.78        14.01         5.29 

$`DEL PEAK 17(6P25.3) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT 
       20.09         0.85        20.78         2.63        20.12         0.99 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79         0.36         0.13         1.12         0.46 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
       44.75        53.85         3.68        41.52        42.77         6.21 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94         3.52         3.68        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        4.08        30.74         4.90        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R 
       21.37        83.24        10.45         0.16         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.13         0.07         0.10         0.07         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.07         0.07         0.10         0.07 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        3.78         8.02         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-V5-A7RE 
       53.95         7.00         4.80 

  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                       122.10                         83.24 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                         3.45                          4.80 
[1] "0.0 - 122.1 (3.5)" "0.1 - 83.2 (4.8)" 
[1] "hr=" "1.4"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6P25.3) MUTATED         4        2        1        0         8
  DEL PEAK 17(6P25.3) WILD-TYPE       3        2        3        1        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6P25.3) MUTATED           6         3          3          2
  DEL PEAK 17(6P25.3) WILD-TYPE        10         8          5          4
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 17(6P25.3) MUTATED            2        0
  DEL PEAK 17(6P25.3) WILD-TYPE          1        1
D43V3, multiclass
            clus
vv           DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  STAGE I                              4                             3
  STAGE IA                             2                             2
  STAGE IB                             1                             3
  STAGE II                             0                             1
  STAGE IIA                            8                            22
  STAGE IIB                            6                            10
  STAGE III                            3                             8
  STAGE IIIA                           3                             5
  STAGE IIIB                           2                             4
  STAGE IIIC                           2                             1
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 17(6P25.3) MUTATED       9  8    16
  DEL PEAK 17(6P25.3) WILD-TYPE    10 18    34
D43V4, multiclass
       clus
vv      DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  T0+T1                           9                            10
  T2                              8                            18
  T3+T4                          16                            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 17(6P25.3) MUTATED   17 11     5
  DEL PEAK 17(6P25.3) WILD-TYPE 33 22     6
D43V5, multiclass
       clus
vv      DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  N0                             17                            33
  N1                             11                            22
  N2+N3                           5                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 17(6P25.3) MUTATED   23   0  9
  DEL PEAK 17(6P25.3) WILD-TYPE 52   1  6
D43V6, multiclass
     clus
vv    DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  M0                           23                            52
  M1A                           0                             1
  MX                            9                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                             0  1
  DEL PEAK 17(6P25.3) MUTATED    6 31
  DEL PEAK 17(6P25.3) WILD-TYPE  9 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED      6   31
  DEL PEAK 17(6P25.3) WILD-TYPE    9   59
        clus
vv       DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  FEMALE                           6                             9
  MALE                            31                            59
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, binary
                               cls
clus                             0  1
  DEL PEAK 17(6P25.3) MUTATED   10 24
  DEL PEAK 17(6P25.3) WILD-TYPE 25 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED     10   24
  DEL PEAK 17(6P25.3) WILD-TYPE   25   42
       clus
vv      DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  ASIAN                          10                            25
  WHITE                          24                            42
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 18(6Q16.3) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 18(6Q16.3) MUTATED   21  7
  DEL PEAK 18(6Q16.3) WILD-TYPE 46 24
  DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE 
                           28                            70 
  DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE 
                            7                            24 
$`DEL PEAK 18(6Q16.3) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB 
       33.27        20.09         0.53         0.46        44.75        60.39 
TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A88Y 
       42.77         3.16         8.94        18.35         3.16         0.36 
TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X 
       16.47        83.24         0.07         0.10         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN 
        0.10         0.10         0.07         0.20         1.18         8.02 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-S8-A6BV TCGA-S8-A6BW 
        5.06        29.59         8.78        14.01 

$`DEL PEAK 18(6Q16.3) WILD-TYPE`
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         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99        17.03         0.79         0.36         0.13         1.12 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E 
      122.10        53.85         3.68        41.52         6.21         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         3.52         3.68         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         6.41         4.08         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       30.74         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       21.37        10.36        10.45         0.16         0.07         0.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.13         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.10         0.07         0.07        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        3.78         7.59        14.70         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         5.29         4.80 

  DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE 
                        4.110                         4.195 
[1] "0.1 - 83.2 (4.1)"  "0.0 - 122.1 (4.2)"
[1] "hr=" "1.8"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(6Q16.3) MUTATED         1        1        1        0         8
  DEL PEAK 18(6Q16.3) WILD-TYPE       6        3        3        1        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(6Q16.3) MUTATED           5         4          2          1
  DEL PEAK 18(6Q16.3) WILD-TYPE        11         7          6          5
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 18(6Q16.3) MUTATED            0        0
  DEL PEAK 18(6Q16.3) WILD-TYPE          3        1
D44V3, multiclass
            clus
vv           DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE
  STAGE I                              1                             6
  STAGE IA                             1                             3
  STAGE IB                             1                             3
  STAGE II                             0                             1
  STAGE IIA                            8                            22
  STAGE IIB                            5                            11
  STAGE III                            4                             7
  STAGE IIIA                           2                             6
  STAGE IIIB                           1                             5
  STAGE IIIC                           0                             3
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 18(6Q16.3) MUTATED       4  8    13
  DEL PEAK 18(6Q16.3) WILD-TYPE    15 18    37
D44V4, multiclass
       clus
vv      DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE
  T0+T1                           4                            15
  T2                              8                            18
  T3+T4                          13                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 18(6Q16.3) MUTATED   13 10     2
  DEL PEAK 18(6Q16.3) WILD-TYPE 37 23     9
D44V5, multiclass
       clus
vv      DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE
  N0                             13                            37
  N1                             10                            23
  N2+N3                           2                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 18(6Q16.3) MUTATED   19   0  5
  DEL PEAK 18(6Q16.3) WILD-TYPE 56   1 10
D44V6, multiclass
     clus
vv    DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE
  M0                           19                            56
  M1A                           0                             1
  MX                            5                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                               cls
clus                             0  1
  DEL PEAK 18(6Q16.3) MUTATED    2 27
  DEL PEAK 18(6Q16.3) WILD-TYPE 13 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q16.3) MUTATED      2   27
  DEL PEAK 18(6Q16.3) WILD-TYPE   13   63
        clus
vv       DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE
  FEMALE                           2                            13
  MALE                            27                            63
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, binary
                               cls
clus                             0  1
  DEL PEAK 18(6Q16.3) MUTATED   13 15
  DEL PEAK 18(6Q16.3) WILD-TYPE 22 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6Q16.3) MUTATED     13   15
  DEL PEAK 18(6Q16.3) WILD-TYPE   22   51
       clus
vv      DEL PEAK 18(6Q16.3) MUTATED DEL PEAK 18(6Q16.3) WILD-TYPE
  ASIAN                          13                            22
  WHITE                          15                            51
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 19(6Q26) MUTATION ANALYSIS
D45V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 19(6Q26) MUTATED   21  5
  DEL PEAK 19(6Q26) WILD-TYPE 46 26
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         26                          72 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                          5                          26 
$`DEL PEAK 19(6Q26) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43J 
       33.27        20.09         0.46        42.77         3.16         4.31 
TCGA-L5-A43M TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NU 
        8.94         3.16         0.36         7.40        16.47        83.24 
TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.10         0.07         0.10         0.13         0.07 
TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6XG 
        0.10         0.10         0.07         1.18         8.02        29.59 
TCGA-S8-A6BW TCGA-V5-A7RE 
       14.01         4.80 

$`DEL PEAK 19(6Q26) WILD-TYPE`
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         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.99         0.53        17.03         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        1.12       122.10        44.75        60.39        53.85         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF 
       41.52         6.21         3.45         0.30         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.35        19.50         8.78         6.41         4.08        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        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        3.95         3.02        21.37        10.36        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
        0.07         0.33         0.13         0.07         0.10         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-M9-A5M8 
        0.10         0.10         0.07         0.07         0.20        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         3.78         7.59         5.06        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        6.35        53.95         9.30         7.00         8.78         5.29 

  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                       0.07                        0.03 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                      83.24                      122.10 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                       3.16                        4.98 
[1] "0.1 - 83.2 (3.2)"  "0.0 - 122.1 (5.0)"
[1] "hr=" "1.8"
D45V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(6Q26) MUTATED         0        1        2        0        12
  DEL PEAK 19(6Q26) WILD-TYPE       7        3        2        1        18
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(6Q26) MUTATED           3         5          0          1
  DEL PEAK 19(6Q26) WILD-TYPE        13         6          8          5
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 19(6Q26) MUTATED            0        0
  DEL PEAK 19(6Q26) WILD-TYPE          3        1
D45V3, multiclass
            clus
vv           DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  STAGE I                            0                           7
  STAGE IA                           1                           3
  STAGE IB                           2                           2
  STAGE II                           0                           1
  STAGE IIA                         12                          18
  STAGE IIB                          3                          13
  STAGE III                          5                           6
  STAGE IIIA                         0                           8
  STAGE IIIB                         1                           5
  STAGE IIIC                         0                           3
  STAGE IV                           0                           1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3+T4
  DEL PEAK 19(6Q26) MUTATED       4  8    14
  DEL PEAK 19(6Q26) WILD-TYPE    15 18    36
D45V4, multiclass
       clus
vv      DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  T0+T1                         4                          15
  T2                            8                          18
  T3+T4                        14                          36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2+N3
  DEL PEAK 19(6Q26) MUTATED   17  7     2
  DEL PEAK 19(6Q26) WILD-TYPE 33 26     9
D45V5, multiclass
       clus
vv      DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  N0                           17                          33
  N1                            7                          26
  N2+N3                         2                           9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1A MX
  DEL PEAK 19(6Q26) MUTATED   21   0  5
  DEL PEAK 19(6Q26) WILD-TYPE 54   1 10
D45V6, multiclass
     clus
vv    DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  M0                         21                          54
  M1A                         0                           1
  MX                          5                          10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                             cls
clus                           0  1
  DEL PEAK 19(6Q26) MUTATED    3 26
  DEL PEAK 19(6Q26) WILD-TYPE 12 64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED      3   26
  DEL PEAK 19(6Q26) WILD-TYPE   12   64
        clus
vv       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  FEMALE                         3                          12
  MALE                          26                          64
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, binary
                             cls
clus                           0  1
  DEL PEAK 19(6Q26) MUTATED   14 14
  DEL PEAK 19(6Q26) WILD-TYPE 21 52
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED     14   14
  DEL PEAK 19(6Q26) WILD-TYPE   21   52
       clus
vv      DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  ASIAN                        14                          21
  WHITE                        14                          52
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 20(7Q31.1) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 20(7Q31.1) MUTATED   24  7
  DEL PEAK 20(7Q31.1) WILD-TYPE 43 24
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           31                            67 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                            7                            24 
$`DEL PEAK 20(7Q31.1) MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 
        0.85         2.63        20.12         0.26        17.03         0.79 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OM 
        0.13         0.46        42.77         3.16         3.68         4.08 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        3.16        29.00         6.94         2.60        25.12         0.36 
TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X 
       16.47        10.36         0.07         0.10         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-R6-A6KZ 
        0.07         0.07         0.10         0.07        17.62         5.06 
TCGA-V5-A7RB 
        5.29 

$`DEL PEAK 20(7Q31.1) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       33.27        20.09        20.78         0.03         0.99         0.53 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.36         1.12       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52         6.21         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94         3.52         3.35        19.50         8.78         6.41 
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        30.74         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.13         7.43         8.71         7.40         3.95         3.02 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       21.37        83.24         0.07        10.45         0.16         0.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.13         0.07         0.10         0.13         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU 
        0.07         0.07         0.10         0.20         1.18         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        3.78         8.02         7.59        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RE 
        4.80 

  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                        42.77                        122.10 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                         2.63                          6.21 
[1] "0.1 - 42.8 (2.6)"  "0.0 - 122.1 (6.2)"
[1] "hr=" "1"  
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(7Q31.1) MUTATED         0        2        2        1         6
  DEL PEAK 20(7Q31.1) WILD-TYPE       7        2        2        0        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(7Q31.1) MUTATED           5         5          3          2
  DEL PEAK 20(7Q31.1) WILD-TYPE        11         6          5          4
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 20(7Q31.1) MUTATED            1        0
  DEL PEAK 20(7Q31.1) WILD-TYPE          2        1
D46V3, multiclass
            clus
vv           DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  STAGE I                              0                             7
  STAGE IA                             2                             2
  STAGE IB                             2                             2
  STAGE II                             1                             0
  STAGE IIA                            6                            24
  STAGE IIB                            5                            11
  STAGE III                            5                             6
  STAGE IIIA                           3                             5
  STAGE IIIB                           2                             4
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 20(7Q31.1) MUTATED       6  5    18
  DEL PEAK 20(7Q31.1) WILD-TYPE    13 21    32
D46V4, multiclass
       clus
vv      DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  T0+T1                           6                            13
  T2                              5                            21
  T3+T4                          18                            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 20(7Q31.1) MUTATED   13 13     3
  DEL PEAK 20(7Q31.1) WILD-TYPE 37 20     8
D46V5, multiclass
       clus
vv      DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  N0                             13                            37
  N1                             13                            20
  N2+N3                           3                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 20(7Q31.1) MUTATED   20   0  7
  DEL PEAK 20(7Q31.1) WILD-TYPE 55   1  8
D46V6, multiclass
     clus
vv    DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  M0                           20                            55
  M1A                           0                             1
  MX                            7                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                               cls
clus                             0  1
  DEL PEAK 20(7Q31.1) MUTATED    1 30
  DEL PEAK 20(7Q31.1) WILD-TYPE 14 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED      1   30
  DEL PEAK 20(7Q31.1) WILD-TYPE   14   60
        clus
vv       DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  FEMALE                           1                            14
  MALE                            30                            60
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, binary
                               cls
clus                             0  1
  DEL PEAK 20(7Q31.1) MUTATED    9 20
  DEL PEAK 20(7Q31.1) WILD-TYPE 26 46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED      9   20
  DEL PEAK 20(7Q31.1) WILD-TYPE   26   46
       clus
vv      DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  ASIAN                           9                            26
  WHITE                          20                            46
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 21(7Q36.2) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 21(7Q36.2) MUTATED   27  9
  DEL PEAK 21(7Q36.2) WILD-TYPE 40 22
  DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE 
                           36                            62 
  DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE 
                            9                            22 
$`DEL PEAK 21(7Q36.2) MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.85        20.12         0.03        17.03         0.79         0.13 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OM 
       53.85         3.68        42.77         3.16         3.68         4.08 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88Y 
       18.35         7.17         3.16        29.00         6.94         0.36 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49X 
       10.36        10.45         0.33         0.10         0.13         0.10 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 
        0.07         0.07         0.10         0.10         0.07         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-V5-A7RB TCGA-V5-A7RE 
       17.62         3.78         5.06        29.59         5.29         4.80 

$`DEL PEAK 21(7Q36.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27        20.09        20.78         2.63         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.53         0.36         1.12         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       60.39        41.52         6.21         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94         3.52         3.35        19.50         8.78         6.41 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         1.38        30.74         4.90         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       16.47        21.37        83.24         0.07         0.16         0.07 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.10         0.07         0.13         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07         0.07         0.20         5.16         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
       14.70         7.04         6.35        53.95         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW 
        8.78        14.01 

  DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE 
                        53.85                        122.10 
  DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE 
                        3.680                         5.685 
[1] "0.0 - 53.9 (3.7)"  "0.1 - 122.1 (5.7)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(7Q36.2) MUTATED         0        3        3        1        11
  DEL PEAK 21(7Q36.2) WILD-TYPE       7        1        1        0        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(7Q36.2) MUTATED           6         4          2          1
  DEL PEAK 21(7Q36.2) WILD-TYPE        10         7          6          5
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 21(7Q36.2) MUTATED            1        0
  DEL PEAK 21(7Q36.2) WILD-TYPE          2        1
D47V3, multiclass
            clus
vv           DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE
  STAGE I                              0                             7
  STAGE IA                             3                             1
  STAGE IB                             3                             1
  STAGE II                             1                             0
  STAGE IIA                           11                            19
  STAGE IIB                            6                            10
  STAGE III                            4                             7
  STAGE IIIA                           2                             6
  STAGE IIIB                           1                             5
  STAGE IIIC                           1                             2
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 21(7Q36.2) MUTATED       9  7    18
  DEL PEAK 21(7Q36.2) WILD-TYPE    10 19    32
D47V4, multiclass
       clus
vv      DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE
  T0+T1                           9                            10
  T2                              7                            19
  T3+T4                          18                            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 21(7Q36.2) MUTATED   20 12     2
  DEL PEAK 21(7Q36.2) WILD-TYPE 30 21     9
D47V5, multiclass
       clus
vv      DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE
  N0                             20                            30
  N1                             12                            21
  N2+N3                           2                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 21(7Q36.2) MUTATED   25   0  6
  DEL PEAK 21(7Q36.2) WILD-TYPE 50   1  9
D47V6, multiclass
     clus
vv    DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE
  M0                           25                            50
  M1A                           0                             1
  MX                            6                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                               cls
clus                             0  1
  DEL PEAK 21(7Q36.2) MUTATED    3 34
  DEL PEAK 21(7Q36.2) WILD-TYPE 12 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.2) MUTATED      3   34
  DEL PEAK 21(7Q36.2) WILD-TYPE   12   56
        clus
vv       DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE
  FEMALE                           3                            12
  MALE                            34                            56
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, binary
                               cls
clus                             0  1
  DEL PEAK 21(7Q36.2) MUTATED   13 22
  DEL PEAK 21(7Q36.2) WILD-TYPE 22 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.2) MUTATED     13   22
  DEL PEAK 21(7Q36.2) WILD-TYPE   22   44
       clus
vv      DEL PEAK 21(7Q36.2) MUTATED DEL PEAK 21(7Q36.2) WILD-TYPE
  ASIAN                          13                            22
  WHITE                          22                            44
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 22(8P23.2) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 22(8P23.2) MUTATED   30 13
  DEL PEAK 22(8P23.2) WILD-TYPE 37 18
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                           43                            55 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                           13                            18 
$`DEL PEAK 22(8P23.2) MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63         0.03         0.26         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH 
        0.79         0.13        44.75        60.39         3.68        42.77 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OT 
        4.31         3.52         3.68        19.50         3.32         4.90 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L7-A6VZ TCGA-LN-A49L 
        7.43         2.60         7.40         3.95        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
        0.16         0.07         0.13         0.07         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.07         0.10         0.10         0.07         0.20         1.18 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RB 
        5.16         3.78         8.02        53.95        14.01         5.29 
TCGA-V5-A7RE 
        4.80 

$`DEL PEAK 22(8P23.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A625 
       33.27        20.09        20.78        20.12         0.99         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-KH-A6WC 
        1.12         0.46       122.10        53.85        41.52         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
        3.16         3.45         0.30         8.94         3.35         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        6.41         4.08        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
       30.74        29.00         7.13         6.94         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K 
        0.36         3.02        16.47        21.37        83.24         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 
        0.33         0.10         0.07         0.10         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.10         0.07         0.07        17.62         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
       14.70         7.04        29.59         6.35         9.30         7.00 
TCGA-S8-A6BV 
        8.78 

  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                        60.39                        122.10 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                         3.52                          6.94 
[1] "0.0 - 60.4 (3.5)"  "0.1 - 122.1 (6.9)"
[1] "hr=" "1.4"
D48V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(8P23.2) MUTATED         2        0        3        0        11
  DEL PEAK 22(8P23.2) WILD-TYPE       5        4        1        1        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(8P23.2) MUTATED          10         5          3          4
  DEL PEAK 22(8P23.2) WILD-TYPE         6         6          5          2
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 22(8P23.2) MUTATED            2        1
  DEL PEAK 22(8P23.2) WILD-TYPE          1        0
D48V3, multiclass
            clus
vv           DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  STAGE I                              2                             5
  STAGE IA                             0                             4
  STAGE IB                             3                             1
  STAGE II                             0                             1
  STAGE IIA                           11                            19
  STAGE IIB                           10                             6
  STAGE III                            5                             6
  STAGE IIIA                           3                             5
  STAGE IIIB                           4                             2
  STAGE IIIC                           2                             1
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 22(8P23.2) MUTATED       7 14    22
  DEL PEAK 22(8P23.2) WILD-TYPE    12 12    28
D48V4, multiclass
       clus
vv      DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  T0+T1                           7                            12
  T2                             14                            12
  T3+T4                          22                            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 22(8P23.2) MUTATED   17 20     6
  DEL PEAK 22(8P23.2) WILD-TYPE 33 13     5
D48V5, multiclass
       clus
vv      DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  N0                             17                            33
  N1                             20                            13
  N2+N3                           6                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 22(8P23.2) MUTATED   35   1  5
  DEL PEAK 22(8P23.2) WILD-TYPE 40   0 10
D48V6, multiclass
     clus
vv    DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  M0                           35                            40
  M1A                           1                             0
  MX                            5                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                               cls
clus                             0  1
  DEL PEAK 22(8P23.2) MUTATED    2 43
  DEL PEAK 22(8P23.2) WILD-TYPE 13 47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED      2   43
  DEL PEAK 22(8P23.2) WILD-TYPE   13   47
        clus
vv       DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  FEMALE                           2                            13
  MALE                            43                            47
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, binary
                               cls
clus                             0  1
  DEL PEAK 22(8P23.2) MUTATED   17 27
  DEL PEAK 22(8P23.2) WILD-TYPE 18 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED     17   27
  DEL PEAK 22(8P23.2) WILD-TYPE   18   39
       clus
vv      DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  ASIAN                          17                            18
  WHITE                          27                            39
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 23(9P21.3) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 23(9P21.3) MUTATED   52 21
  DEL PEAK 23(9P21.3) WILD-TYPE 15 10
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                           73                            25 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                           21                            10 
$`DEL PEAK 23(9P21.3) MUTATED`
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         0.03 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.53        17.03         0.79         0.36         0.13 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
        0.46        44.75        60.39         3.16         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        8.94         3.68        19.50         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17        30.74         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        6.94         2.60         0.36         3.95         3.02        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       21.37        83.24        10.36         0.07        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        0.07         0.33         0.10         0.13         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.07         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 
        1.18        17.62         5.16         3.78         5.06        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       29.59         6.35         9.30         8.78        14.01         5.29 
TCGA-V5-A7RE 
        4.80 

$`DEL PEAK 23(9P21.3) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
       20.09         0.99         1.12       122.10        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OG 
       41.52        42.77         6.21         3.45         3.52         3.35 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A88T TCGA-L5-A88W 
        8.78         6.41         1.38         3.16         8.71        25.12 
TCGA-L5-A88Z TCGA-LN-A49V TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y0 
        7.40         0.10         8.02         7.59         7.04        53.95 
TCGA-RE-A7BO 
        7.00 

  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                         0.03                          0.10 
  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 
                         3.68                          7.04 
[1] "0.0 - 83.2 (3.7)"  "0.1 - 122.1 (7.0)"
[1] "hr=" "1.2"
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P21.3) MUTATED         3        2        4        1        25
  DEL PEAK 23(9P21.3) WILD-TYPE       4        2        0        0         5
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9P21.3) MUTATED          12         9          6          5
  DEL PEAK 23(9P21.3) WILD-TYPE         4         2          2          1
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 23(9P21.3) MUTATED            2        1
  DEL PEAK 23(9P21.3) WILD-TYPE          1        0
D49V3, multiclass
            clus
vv           DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  STAGE I                              3                             4
  STAGE IA                             2                             2
  STAGE IB                             4                             0
  STAGE II                             1                             0
  STAGE IIA                           25                             5
  STAGE IIB                           12                             4
  STAGE III                            9                             2
  STAGE IIIA                           6                             2
  STAGE IIIB                           5                             1
  STAGE IIIC                           2                             1
  STAGE IV                             1                             0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 23(9P21.3) MUTATED      11 23    40
  DEL PEAK 23(9P21.3) WILD-TYPE     8  3    10
D49V4, multiclass
       clus
vv      DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  T0+T1                          11                             8
  T2                             23                             3
  T3+T4                          40                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 23(9P21.3) MUTATED   39 27     8
  DEL PEAK 23(9P21.3) WILD-TYPE 11  6     3
D49V5, multiclass
       clus
vv      DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  N0                             39                            11
  N1                             27                             6
  N2+N3                           8                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 23(9P21.3) MUTATED   60   1 10
  DEL PEAK 23(9P21.3) WILD-TYPE 15   0  5
D49V6, multiclass
     clus
vv    DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  M0                           60                            15
  M1A                           1                             0
  MX                           10                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                               cls
clus                             0  1
  DEL PEAK 23(9P21.3) MUTATED    8 72
  DEL PEAK 23(9P21.3) WILD-TYPE  7 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED      8   72
  DEL PEAK 23(9P21.3) WILD-TYPE    7   18
        clus
vv       DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  FEMALE                           8                             7
  MALE                            72                            18
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, binary
                               cls
clus                             0  1
  DEL PEAK 23(9P21.3) MUTATED   33 43
  DEL PEAK 23(9P21.3) WILD-TYPE  2 23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     33   43
  DEL PEAK 23(9P21.3) WILD-TYPE    2   23
       clus
vv      DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  ASIAN                          33                             2
  WHITE                          43                            23
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 24(10P15.1) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(10P15.1) MUTATED   16  9
  DEL PEAK 24(10P15.1) WILD-TYPE 51 22
  DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE 
                            25                             73 
  DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE 
                             9                             22 
$`DEL PEAK 24(10P15.1) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A43H 
       33.27         0.85         0.03         0.53         0.79         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OO 
        4.31         8.94         3.52         3.68         3.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A88V TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49O 
        3.16         4.90         2.60        83.24         0.07         0.33 
TCGA-LN-A49W TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-Q9-A6FW 
        0.07         0.07         0.10         0.07         1.18         3.78 
TCGA-V5-A7RE 
        4.80 

$`DEL PEAK 24(10P15.1) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09        20.78         2.63        20.12         0.26         0.99 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
       17.03         0.36         0.13         1.12         0.46       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        53.85         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        6.21         3.16         3.45        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        4.08        18.35         7.17         1.38        30.74        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         7.43         6.94         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L7-A6VZ 
        7.40         3.95         3.02        16.47        21.37        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45         0.16         0.07         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.10         0.07         0.20        17.62         5.16 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB 
        5.29 

  DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE 
                          2.60                           6.94 
[1] "0.0 - 83.2 (2.6)"  "0.1 - 122.1 (6.9)"
[1] "hr=" "2.4"
D50V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(10P15.1) MUTATED         1        1        2        0         8
  DEL PEAK 24(10P15.1) WILD-TYPE       6        3        2        1        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10P15.1) MUTATED           3         4          2          2
  DEL PEAK 24(10P15.1) WILD-TYPE        13         7          6          4
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 24(10P15.1) MUTATED            1        1
  DEL PEAK 24(10P15.1) WILD-TYPE          2        0
D50V3, multiclass
            clus
vv           DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE
  STAGE I                               1                              6
  STAGE IA                              1                              3
  STAGE IB                              2                              2
  STAGE II                              0                              1
  STAGE IIA                             8                             22
  STAGE IIB                             3                             13
  STAGE III                             4                              7
  STAGE IIIA                            2                              6
  STAGE IIIB                            2                              4
  STAGE IIIC                            1                              2
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 24(10P15.1) MUTATED       4  6    16
  DEL PEAK 24(10P15.1) WILD-TYPE    15 20    34
D50V4, multiclass
       clus
vv      DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE
  T0+T1                            4                             15
  T2                               6                             20
  T3+T4                           16                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 24(10P15.1) MUTATED   14  8     4
  DEL PEAK 24(10P15.1) WILD-TYPE 36 25     7
D50V5, multiclass
       clus
vv      DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE
  N0                              14                             36
  N1                               8                             25
  N2+N3                            4                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 24(10P15.1) MUTATED   19   1  4
  DEL PEAK 24(10P15.1) WILD-TYPE 56   0 11
D50V6, multiclass
     clus
vv    DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE
  M0                            19                             56
  M1A                            1                              0
  MX                             4                             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(10P15.1) MUTATED    3 23
  DEL PEAK 24(10P15.1) WILD-TYPE 12 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.1) MUTATED      3   23
  DEL PEAK 24(10P15.1) WILD-TYPE   12   67
        clus
vv       DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE
  FEMALE                            3                             12
  MALE                             23                             67
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, binary
                                cls
clus                              0  1
  DEL PEAK 24(10P15.1) MUTATED    9 16
  DEL PEAK 24(10P15.1) WILD-TYPE 26 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.1) MUTATED      9   16
  DEL PEAK 24(10P15.1) WILD-TYPE   26   50
       clus
vv      DEL PEAK 24(10P15.1) MUTATED DEL PEAK 24(10P15.1) WILD-TYPE
  ASIAN                            9                             26
  WHITE                           16                             50
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 25(10P11.21) MUTATION ANALYSIS
D51V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 25(10P11.21) MUTATED   10  8
  DEL PEAK 25(10P11.21) WILD-TYPE 57 23
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             18                              80 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                              8                              23 
$`DEL PEAK 25(10P11.21) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-JY-A6FA 
       33.27         0.85         0.03         0.53         0.79        44.75 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OT TCGA-L5-A8NU 
        0.30         4.31         3.52         3.35         4.90        83.24 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 
        0.33         0.13         0.10         0.07         0.07         1.18 

$`DEL PEAK 25(10P11.21) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09        20.78         2.63        20.12         0.26         0.99 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
       17.03         0.36         0.13         1.12         0.46       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
       60.39        53.85         3.68        41.52        42.77         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        3.16         3.45         8.94         3.68        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        6.41         4.08        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        30.74        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        3.02        16.47        21.37        10.36         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
        0.16         0.07         0.10         0.07         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.10         0.20        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                           0.03                            0.07 
  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 
                           0.82                            5.75 
[1] "0.0 - 83.2 (0.8)"  "0.1 - 122.1 (5.8)"
[1] "hr=" "2.2"
D51V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(10P11.21) MUTATED         1        0        1        0        11
  DEL PEAK 25(10P11.21) WILD-TYPE       6        4        3        1        19
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10P11.21) MUTATED           3         1          2          1
  DEL PEAK 25(10P11.21) WILD-TYPE        13        10          6          5
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 25(10P11.21) MUTATED            0        1
  DEL PEAK 25(10P11.21) WILD-TYPE          3        0
D51V3, multiclass
            clus
vv           DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  STAGE I                                1                               6
  STAGE IA                               0                               4
  STAGE IB                               1                               3
  STAGE II                               0                               1
  STAGE IIA                             11                              19
  STAGE IIB                              3                              13
  STAGE III                              1                              10
  STAGE IIIA                             2                               6
  STAGE IIIB                             1                               5
  STAGE IIIC                             0                               3
  STAGE IV                               1                               0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3+T4
  DEL PEAK 25(10P11.21) MUTATED       1  8    12
  DEL PEAK 25(10P11.21) WILD-TYPE    18 18    38
D51V4, multiclass
       clus
vv      DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  T0+T1                             1                              18
  T2                                8                              18
  T3+T4                            12                              38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 25(10P11.21) MUTATED   15  5     1
  DEL PEAK 25(10P11.21) WILD-TYPE 35 28    10
D51V5, multiclass
       clus
vv      DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  N0                               15                              35
  N1                                5                              28
  N2+N3                             1                              10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1A MX
  DEL PEAK 25(10P11.21) MUTATED   18   1  1
  DEL PEAK 25(10P11.21) WILD-TYPE 57   0 14
D51V6, multiclass
     clus
vv    DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  M0                             18                              57
  M1A                             1                               0
  MX                              1                              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10P11.21) MUTATED    2 19
  DEL PEAK 25(10P11.21) WILD-TYPE 13 71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED      2   19
  DEL PEAK 25(10P11.21) WILD-TYPE   13   71
        clus
vv       DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  FEMALE                             2                              13
  MALE                              19                              71
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10P11.21) MUTATED   11 10
  DEL PEAK 25(10P11.21) WILD-TYPE 24 56
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED     11   10
  DEL PEAK 25(10P11.21) WILD-TYPE   24   56
       clus
vv      DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  ASIAN                            11                              24
  WHITE                            10                              56
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 26(10Q22.3) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(10Q22.3) MUTATED   20  8
  DEL PEAK 26(10Q22.3) WILD-TYPE 47 23
  DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE 
                            28                             70 
  DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE 
                             8                             23 
$`DEL PEAK 26(10Q22.3) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-L5-A43C 
       33.27        20.09         0.85         2.63         0.53         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OQ 
        0.30         4.31         3.52         3.35         6.41         1.38 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y 
        4.90         7.13        83.24         0.16         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.13         0.10         0.10         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6Y0 TCGA-V5-A7RE 
        1.18         5.16        53.95         4.80 

$`DEL PEAK 26(10Q22.3) WILD-TYPE`
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       20.78        20.12         0.03         0.26         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.79         0.36         0.13         1.12         0.46       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        53.85         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        6.21         3.45         8.94         3.68        19.50         8.78 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
        4.08        18.35         3.32         7.17         3.16        30.74 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ 
        0.36         7.40         3.95         3.02        16.47        21.37 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       10.36         0.07        10.45         0.07         0.33         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.10         0.07         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07         0.07        17.62         3.78         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        5.06        14.70         7.04        29.59         6.35         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        7.00         8.78        14.01         5.29 

  DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE 
                         2.005                          6.645 
[1] "0.1 - 83.2 (2.0)"  "0.0 - 122.1 (6.6)"
[1] "hr=" "1.3"
D52V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(10Q22.3) MUTATED         2        0        1        1        11
  DEL PEAK 26(10Q22.3) WILD-TYPE       5        4        3        0        19
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10Q22.3) MUTATED           4         4          4          2
  DEL PEAK 26(10Q22.3) WILD-TYPE        12         7          4          4
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 26(10Q22.3) MUTATED            0        1
  DEL PEAK 26(10Q22.3) WILD-TYPE          3        0
D52V3, multiclass
            clus
vv           DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE
  STAGE I                               2                              5
  STAGE IA                              0                              4
  STAGE IB                              1                              3
  STAGE II                              1                              0
  STAGE IIA                            11                             19
  STAGE IIB                             4                             12
  STAGE III                             4                              7
  STAGE IIIA                            4                              4
  STAGE IIIB                            2                              4
  STAGE IIIC                            0                              3
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 26(10Q22.3) MUTATED       3 11    16
  DEL PEAK 26(10Q22.3) WILD-TYPE    16 15    34
D52V4, multiclass
       clus
vv      DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE
  T0+T1                            3                             16
  T2                              11                             15
  T3+T4                           16                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 26(10Q22.3) MUTATED   18  9     3
  DEL PEAK 26(10Q22.3) WILD-TYPE 32 24     8
D52V5, multiclass
       clus
vv      DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE
  N0                              18                             32
  N1                               9                             24
  N2+N3                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 26(10Q22.3) MUTATED   26   1  2
  DEL PEAK 26(10Q22.3) WILD-TYPE 49   0 13
D52V6, multiclass
     clus
vv    DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE
  M0                            26                             49
  M1A                            1                              0
  MX                             2                             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(10Q22.3) MUTATED    5 27
  DEL PEAK 26(10Q22.3) WILD-TYPE 10 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q22.3) MUTATED      5   27
  DEL PEAK 26(10Q22.3) WILD-TYPE   10   63
        clus
vv       DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE
  FEMALE                            5                             10
  MALE                             27                             63
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, binary
                                cls
clus                              0  1
  DEL PEAK 26(10Q22.3) MUTATED   15 16
  DEL PEAK 26(10Q22.3) WILD-TYPE 20 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q22.3) MUTATED     15   16
  DEL PEAK 26(10Q22.3) WILD-TYPE   20   50
       clus
vv      DEL PEAK 26(10Q22.3) MUTATED DEL PEAK 26(10Q22.3) WILD-TYPE
  ASIAN                           15                             20
  WHITE                           16                             50
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 27(10Q23.31) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 27(10Q23.31) MUTATED   24 12
  DEL PEAK 27(10Q23.31) WILD-TYPE 43 19
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             36                              62 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             12                              19 
$`DEL PEAK 27(10Q23.31) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-JY-A6FA 
       33.27        20.09         0.85         2.63         0.53        44.75 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
        3.16         0.30         4.31         8.94         3.52         3.35 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       19.50         6.41         3.32         3.16        30.74         4.90 
TCGA-L5-A4OW TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y 
        7.13        83.24        10.45         0.16         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.13         0.10         0.10         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-V5-A7RE 
        1.18         5.16         7.59         5.06        53.95         4.80 

$`DEL PEAK 27(10Q23.31) WILD-TYPE`
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       20.78        20.12         0.03         0.26         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.79         0.36         0.13         1.12         0.46       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
       60.39        53.85         3.68        41.52        42.77         6.21 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        3.45         3.68         8.78         4.08        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        1.38        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
       25.12         0.36         7.40         3.95         3.02        16.47 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       21.37        10.36         0.07         0.07         0.33         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.10         0.07         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 
        0.07         0.07        17.62         3.78         8.02        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04        29.59         6.35         9.30         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB 
       14.01         5.29 

  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                           0.07                            0.03 
  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 
                          3.435                           5.750 
[1] "0.1 - 83.2 (3.4)"  "0.0 - 122.1 (5.8)"
[1] "hr=" "1.2"
D53V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10Q23.31) MUTATED         3        1        1        1        12
  DEL PEAK 27(10Q23.31) WILD-TYPE       4        3        3        0        18
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10Q23.31) MUTATED           6         4          3          2
  DEL PEAK 27(10Q23.31) WILD-TYPE        10         7          5          4
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 27(10Q23.31) MUTATED            1        1
  DEL PEAK 27(10Q23.31) WILD-TYPE          2        0
D53V3, multiclass
            clus
vv           DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  STAGE I                                3                               4
  STAGE IA                               1                               3
  STAGE IB                               1                               3
  STAGE II                               1                               0
  STAGE IIA                             12                              18
  STAGE IIB                              6                              10
  STAGE III                              4                               7
  STAGE IIIA                             3                               5
  STAGE IIIB                             2                               4
  STAGE IIIC                             1                               2
  STAGE IV                               1                               0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3+T4
  DEL PEAK 27(10Q23.31) MUTATED       5 13    18
  DEL PEAK 27(10Q23.31) WILD-TYPE    14 13    32
D53V4, multiclass
       clus
vv      DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  T0+T1                             5                              14
  T2                               13                              13
  T3+T4                            18                              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 27(10Q23.31) MUTATED   21 11     4
  DEL PEAK 27(10Q23.31) WILD-TYPE 29 22     7
D53V5, multiclass
       clus
vv      DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  N0                               21                              29
  N1                               11                              22
  N2+N3                             4                               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1A MX
  DEL PEAK 27(10Q23.31) MUTATED   31   1  3
  DEL PEAK 27(10Q23.31) WILD-TYPE 44   0 12
D53V6, multiclass
     clus
vv    DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  M0                             31                              44
  M1A                             1                               0
  MX                              3                              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                                 cls
clus                               0  1
  DEL PEAK 27(10Q23.31) MUTATED    8 32
  DEL PEAK 27(10Q23.31) WILD-TYPE  7 58
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED      8   32
  DEL PEAK 27(10Q23.31) WILD-TYPE    7   58
        clus
vv       DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  FEMALE                             8                               7
  MALE                              32                              58
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, binary
                                 cls
clus                               0  1
  DEL PEAK 27(10Q23.31) MUTATED   17 21
  DEL PEAK 27(10Q23.31) WILD-TYPE 18 45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED     17   21
  DEL PEAK 27(10Q23.31) WILD-TYPE   18   45
       clus
vv      DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  ASIAN                            17                              18
  WHITE                            21                              45
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 28(11P15.4) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(11P15.4) MUTATED   34  6
  DEL PEAK 28(11P15.4) WILD-TYPE 33 25
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            40                             58 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                             6                             25 
$`DEL PEAK 28(11P15.4) MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
        0.85         2.63         0.53         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP 
        4.31         8.94         3.35        19.50         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        3.16         6.94         2.60         0.36         3.95         3.02 
TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       16.47        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A4A2 
        0.33         0.10         0.13         0.07         0.10         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.07         0.10         0.10         0.07         0.20         1.18 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-V5-A7RE 
       29.59        53.95         8.78         4.80 

$`DEL PEAK 28(11P15.4) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27        20.09        20.78        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99        17.03         0.79         0.36         0.13         1.12 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.46       122.10        44.75        60.39        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI 
       41.52        42.77         6.21         3.52         3.68         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
        6.41         4.08        18.35         1.38        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.13         7.43         8.71        25.12         7.40 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A4 
       21.37        83.24         0.10         0.07         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.07         0.07        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        14.70         7.04         6.35 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30         7.00        14.01         5.29 

  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                         53.95                         122.10 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                         2.615                          7.020 
[1] "0.1 - 54.0 (2.6)"  "0.0 - 122.1 (7.0)"
[1] "hr=" "1.4"
D54V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(11P15.4) MUTATED         4        2        2        1        13
  DEL PEAK 28(11P15.4) WILD-TYPE       3        2        2        0        17
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(11P15.4) MUTATED           3         7          4          0
  DEL PEAK 28(11P15.4) WILD-TYPE        13         4          4          6
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 28(11P15.4) MUTATED            2        0
  DEL PEAK 28(11P15.4) WILD-TYPE          1        1
D54V3, multiclass
            clus
vv           DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  STAGE I                               4                              3
  STAGE IA                              2                              2
  STAGE IB                              2                              2
  STAGE II                              1                              0
  STAGE IIA                            13                             17
  STAGE IIB                             3                             13
  STAGE III                             7                              4
  STAGE IIIA                            4                              4
  STAGE IIIB                            0                              6
  STAGE IIIC                            2                              1
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 28(11P15.4) MUTATED       8  8    25
  DEL PEAK 28(11P15.4) WILD-TYPE    11 18    25
D54V4, multiclass
       clus
vv      DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  T0+T1                            8                             11
  T2                               8                             18
  T3+T4                           25                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 28(11P15.4) MUTATED   25 13     3
  DEL PEAK 28(11P15.4) WILD-TYPE 25 20     8
D54V5, multiclass
       clus
vv      DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  N0                              25                             25
  N1                              13                             20
  N2+N3                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 28(11P15.4) MUTATED   32   0  9
  DEL PEAK 28(11P15.4) WILD-TYPE 43   1  6
D54V6, multiclass
     clus
vv    DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  M0                            32                             43
  M1A                            0                              1
  MX                             9                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED    4 40
  DEL PEAK 28(11P15.4) WILD-TYPE 11 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED      4   40
  DEL PEAK 28(11P15.4) WILD-TYPE   11   50
        clus
vv       DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  FEMALE                            4                             11
  MALE                             40                             50
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED   21 22
  DEL PEAK 28(11P15.4) WILD-TYPE 14 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED     21   22
  DEL PEAK 28(11P15.4) WILD-TYPE   14   44
       clus
vv      DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  ASIAN                           21                             14
  WHITE                           22                             44
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 29(11Q24.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 29(11Q24.3) MUTATED   31  9
  DEL PEAK 29(11Q24.3) WILD-TYPE 36 22
  DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE 
                            40                             58 
  DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE 
                             9                             22 
$`DEL PEAK 29(11Q24.3) MUTATED`
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A6QS TCGA-JY-A6FH 
       20.12         0.03         0.26        17.03         0.13        42.77 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        3.16         0.30         3.68         4.08         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
        3.16        29.00         6.94         2.60         3.95         3.02 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       10.36         0.07        10.45         0.16         0.07         0.10 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU 
        0.07         0.10         0.07         0.20         1.18         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-S8-A6BV 
        3.78         8.02         5.06         8.78 

$`DEL PEAK 29(11Q24.3) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT 
       33.27        20.09         0.85        20.78         2.63         0.99 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.53         0.79         0.36         1.12         0.46       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
       44.75        60.39        53.85         3.68        41.52         6.21 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
        3.45         4.31         8.94         3.52         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
        8.78         6.41        18.35         1.38        30.74         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         7.43         8.71        25.12         0.36         7.40 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       16.47        21.37        83.24         0.33         0.13         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-R6-A6DQ 
        0.10         0.07         0.10         0.07        17.62         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        7.00        14.01         5.29         4.80 

  DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE 
                         42.77                         122.10 
  DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE 
                          2.81                           7.02 
[1] "0.0 - 42.8 (2.8)"  "0.1 - 122.1 (7.0)"
[1] "hr=" "1.3"
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(11Q24.3) MUTATED         1        3        1        1        13
  DEL PEAK 29(11Q24.3) WILD-TYPE       6        1        3        0        17
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(11Q24.3) MUTATED           7         6          2          3
  DEL PEAK 29(11Q24.3) WILD-TYPE         9         5          6          3
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 29(11Q24.3) MUTATED            2        0
  DEL PEAK 29(11Q24.3) WILD-TYPE          1        1
D55V3, multiclass
            clus
vv           DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE
  STAGE I                               1                              6
  STAGE IA                              3                              1
  STAGE IB                              1                              3
  STAGE II                              1                              0
  STAGE IIA                            13                             17
  STAGE IIB                             7                              9
  STAGE III                             6                              5
  STAGE IIIA                            2                              6
  STAGE IIIB                            3                              3
  STAGE IIIC                            2                              1
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 29(11Q24.3) MUTATED       6 14    20
  DEL PEAK 29(11Q24.3) WILD-TYPE    13 12    30
D55V4, multiclass
       clus
vv      DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE
  T0+T1                            6                             13
  T2                              14                             12
  T3+T4                           20                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 29(11Q24.3) MUTATED   19 16     5
  DEL PEAK 29(11Q24.3) WILD-TYPE 31 17     6
D55V5, multiclass
       clus
vv      DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE
  N0                              19                             31
  N1                              16                             17
  N2+N3                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 29(11Q24.3) MUTATED   32   0  6
  DEL PEAK 29(11Q24.3) WILD-TYPE 43   1  9
D55V6, multiclass
     clus
vv    DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE
  M0                            32                             43
  M1A                            0                              1
  MX                             6                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                cls
clus                              0  1
  DEL PEAK 29(11Q24.3) MUTATED    4 39
  DEL PEAK 29(11Q24.3) WILD-TYPE 11 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11Q24.3) MUTATED      4   39
  DEL PEAK 29(11Q24.3) WILD-TYPE   11   51
        clus
vv       DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE
  FEMALE                            4                             11
  MALE                             39                             51
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, binary
                                cls
clus                              0  1
  DEL PEAK 29(11Q24.3) MUTATED   19 24
  DEL PEAK 29(11Q24.3) WILD-TYPE 16 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11Q24.3) MUTATED     19   24
  DEL PEAK 29(11Q24.3) WILD-TYPE   16   42
       clus
vv      DEL PEAK 29(11Q24.3) MUTATED DEL PEAK 29(11Q24.3) WILD-TYPE
  ASIAN                           19                             16
  WHITE                           24                             42
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 30(12Q21.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(12Q21.2) MUTATED   18  4
  DEL PEAK 30(12Q21.2) WILD-TYPE 49 27
  DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE 
                            22                             76 
  DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE 
                             4                             27 
$`DEL PEAK 30(12Q21.2) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 
       33.27        20.09         2.63         0.03         0.26         0.79 
TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP 
       42.77         3.45         8.94        19.50         6.41         7.17 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 
       30.74         7.13         6.94         2.60         0.36         3.02 
TCGA-LN-A5U6 TCGA-Q9-A6FW TCGA-S8-A6BV TCGA-S8-A6BW 
        0.20         3.78         8.78        14.01 

$`DEL PEAK 30(12Q21.2) WILD-TYPE`
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.78        20.12         0.99         0.53        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.36         0.13         1.12         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C 
       60.39        53.85         3.68        41.52         6.21         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
        0.30         4.31         3.52         3.68         3.35         8.78 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
        4.08        18.35         3.32         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
       29.00         7.43         8.71        25.12         7.40         3.95 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       16.47        21.37        83.24        10.36         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.16         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07         1.18        17.62         5.16         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         5.29         4.80 

  DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE 
                         42.77                         122.10 
  DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE 
                         6.675                          4.015 
[1] "0.0 - 42.8 (6.7)"  "0.1 - 122.1 (4.0)"
[1] "hr=" "2"  
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(12Q21.2) MUTATED         4        1        3        0         3
  DEL PEAK 30(12Q21.2) WILD-TYPE       3        3        1        1        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(12Q21.2) MUTATED           6         1          2          2
  DEL PEAK 30(12Q21.2) WILD-TYPE        10        10          6          4
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 30(12Q21.2) MUTATED            0        0
  DEL PEAK 30(12Q21.2) WILD-TYPE          3        1
D56V3, multiclass
            clus
vv           DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE
  STAGE I                               4                              3
  STAGE IA                              1                              3
  STAGE IB                              3                              1
  STAGE II                              0                              1
  STAGE IIA                             3                             27
  STAGE IIB                             6                             10
  STAGE III                             1                             10
  STAGE IIIA                            2                              6
  STAGE IIIB                            2                              4
  STAGE IIIC                            0                              3
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 30(12Q21.2) MUTATED       6  7    11
  DEL PEAK 30(12Q21.2) WILD-TYPE    13 19    39
D56V4, multiclass
       clus
vv      DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE
  T0+T1                            6                             13
  T2                               7                             19
  T3+T4                           11                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 30(12Q21.2) MUTATED   13  8     3
  DEL PEAK 30(12Q21.2) WILD-TYPE 37 25     8
D56V5, multiclass
       clus
vv      DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE
  N0                              13                             37
  N1                               8                             25
  N2+N3                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 30(12Q21.2) MUTATED   17   0  7
  DEL PEAK 30(12Q21.2) WILD-TYPE 58   1  8
D56V6, multiclass
     clus
vv    DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE
  M0                            17                             58
  M1A                            0                              1
  MX                             7                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                cls
clus                              0  1
  DEL PEAK 30(12Q21.2) MUTATED    7 17
  DEL PEAK 30(12Q21.2) WILD-TYPE  8 73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q21.2) MUTATED      7   17
  DEL PEAK 30(12Q21.2) WILD-TYPE    8   73
        clus
vv       DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE
  FEMALE                            7                              8
  MALE                             17                             73
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, binary
                                cls
clus                              0  1
  DEL PEAK 30(12Q21.2) MUTATED    3 19
  DEL PEAK 30(12Q21.2) WILD-TYPE 32 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q21.2) MUTATED      3   19
  DEL PEAK 30(12Q21.2) WILD-TYPE   32   47
       clus
vv      DEL PEAK 30(12Q21.2) MUTATED DEL PEAK 30(12Q21.2) WILD-TYPE
  ASIAN                            3                             32
  WHITE                           19                             47
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 31(13Q12.11) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 31(13Q12.11) MUTATED   30 11
  DEL PEAK 31(13Q12.11) WILD-TYPE 37 20
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             41                              57 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             11                              20 
$`DEL PEAK 31(13Q12.11) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A51D 
       20.09         0.85        20.78         2.63         0.26        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43M 
        0.79         0.13         0.46        60.39        53.85         8.94 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S 
        3.68         4.08         3.16         4.90        29.00         6.94 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 
        0.33         0.10         0.13         0.07         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 
        0.07         0.10         0.10         0.10         0.07         0.20 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-V5-A7RE 
        5.16         5.06        29.59         6.35         4.80 

$`DEL PEAK 31(13Q12.11) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A625 
       33.27        20.12         0.03         0.99         0.53         0.36 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        1.12       122.10        44.75         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
        6.21         3.16         3.45         0.30         4.31         3.52 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        3.35        19.50         8.78         6.41        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        7.17         1.38        30.74         7.13         7.43         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A8 
       16.47        21.37         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.10         0.07         1.18        17.62         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.59        14.70         7.04        53.95         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        8.78        14.01         5.29 

  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                           0.07                            0.03 
  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 
                           2.63                            6.41 
[1] "0.1 - 83.2 (2.6)"  "0.0 - 122.1 (6.4)"
[1] "hr=" "1"  
D57V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(13Q12.11) MUTATED         1        2        3        1        14
  DEL PEAK 31(13Q12.11) WILD-TYPE       6        2        1        0        16
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(13Q12.11) MUTATED           6         5          3          3
  DEL PEAK 31(13Q12.11) WILD-TYPE        10         6          5          3
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 31(13Q12.11) MUTATED            1        1
  DEL PEAK 31(13Q12.11) WILD-TYPE          2        0
D57V3, multiclass
            clus
vv           DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  STAGE I                                1                               6
  STAGE IA                               2                               2
  STAGE IB                               3                               1
  STAGE II                               1                               0
  STAGE IIA                             14                              16
  STAGE IIB                              6                              10
  STAGE III                              5                               6
  STAGE IIIA                             3                               5
  STAGE IIIB                             3                               3
  STAGE IIIC                             1                               2
  STAGE IV                               1                               0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3+T4
  DEL PEAK 31(13Q12.11) MUTATED       6 11    24
  DEL PEAK 31(13Q12.11) WILD-TYPE    13 15    26
D57V4, multiclass
       clus
vv      DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  T0+T1                             6                              13
  T2                               11                              15
  T3+T4                            24                              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 31(13Q12.11) MUTATED   24 12     5
  DEL PEAK 31(13Q12.11) WILD-TYPE 26 21     6
D57V5, multiclass
       clus
vv      DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  N0                               24                              26
  N1                               12                              21
  N2+N3                             5                               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1A MX
  DEL PEAK 31(13Q12.11) MUTATED   34   1  4
  DEL PEAK 31(13Q12.11) WILD-TYPE 41   0 11
D57V6, multiclass
     clus
vv    DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  M0                             34                              41
  M1A                             1                               0
  MX                              4                              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED    4 40
  DEL PEAK 31(13Q12.11) WILD-TYPE 11 50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED      4   40
  DEL PEAK 31(13Q12.11) WILD-TYPE   11   50
        clus
vv       DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  FEMALE                             4                              11
  MALE                              40                              50
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED   21 22
  DEL PEAK 31(13Q12.11) WILD-TYPE 14 44
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED     21   22
  DEL PEAK 31(13Q12.11) WILD-TYPE   14   44
       clus
vv      DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  ASIAN                            21                              14
  WHITE                            22                              44
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 32(13Q14.2) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 32(13Q14.2) MUTATED   34 10
  DEL PEAK 32(13Q14.2) WILD-TYPE 33 21
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            44                             54 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            10                             21 
$`DEL PEAK 32(13Q14.2) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         0.85        20.78         2.63         0.26         0.53 
TCGA-IG-A51D TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       17.03         0.13        44.75        60.39        53.85         3.68 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
        3.52         3.68         6.41         4.08         3.16        29.00 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        3.95         3.02        83.24        10.36         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.16         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6KZ TCGA-R6-A6XG 
        0.10         0.07         0.07         0.20         5.06        29.59 
TCGA-R6-A6XQ TCGA-V5-A7RE 
        6.35         4.80 

$`DEL PEAK 32(13Q14.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 
       33.27        20.12         0.03         0.99         0.79         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
        1.12         0.46       122.10        41.52        42.77         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
        3.16         3.45         0.30         4.31         8.94         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.50         8.78        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-A88T 
       30.74         4.90         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NQ 
        2.60        25.12         0.36         7.40        16.47        21.37 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.10         0.07         0.07         0.10         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         3.78         8.02         7.59        14.70         7.04 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30         7.00         8.78        14.01         5.29 

  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                          0.07                           0.03 
  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 
                         2.825                          7.020 
[1] "0.1 - 83.2 (2.8)"  "0.0 - 122.1 (7.0)"
[1] "hr=" "1.2"
D58V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(13Q14.2) MUTATED         3        2        1        1        16
  DEL PEAK 32(13Q14.2) WILD-TYPE       4        2        3        0        14
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(13Q14.2) MUTATED           7         6          4          2
  DEL PEAK 32(13Q14.2) WILD-TYPE         9         5          4          4
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 32(13Q14.2) MUTATED            1        0
  DEL PEAK 32(13Q14.2) WILD-TYPE          2        1
D58V3, multiclass
            clus
vv           DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  STAGE I                               3                              4
  STAGE IA                              2                              2
  STAGE IB                              1                              3
  STAGE II                              1                              0
  STAGE IIA                            16                             14
  STAGE IIB                             7                              9
  STAGE III                             6                              5
  STAGE IIIA                            4                              4
  STAGE IIIB                            2                              4
  STAGE IIIC                            1                              2
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 32(13Q14.2) MUTATED       8 13    23
  DEL PEAK 32(13Q14.2) WILD-TYPE    11 13    27
D58V4, multiclass
       clus
vv      DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  T0+T1                            8                             11
  T2                              13                             13
  T3+T4                           23                             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 32(13Q14.2) MUTATED   26 15     3
  DEL PEAK 32(13Q14.2) WILD-TYPE 24 18     8
D58V5, multiclass
       clus
vv      DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  N0                              26                             24
  N1                              15                             18
  N2+N3                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 32(13Q14.2) MUTATED   39   0  2
  DEL PEAK 32(13Q14.2) WILD-TYPE 36   1 13
D58V6, multiclass
     clus
vv    DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  M0                            39                             36
  M1A                            0                              1
  MX                             2                             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED    4 43
  DEL PEAK 32(13Q14.2) WILD-TYPE 11 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED      4   43
  DEL PEAK 32(13Q14.2) WILD-TYPE   11   47
        clus
vv       DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  FEMALE                            4                             11
  MALE                             43                             47
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED   24 23
  DEL PEAK 32(13Q14.2) WILD-TYPE 11 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     24   23
  DEL PEAK 32(13Q14.2) WILD-TYPE   11   43
       clus
vv      DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  ASIAN                           24                             11
  WHITE                           23                             43
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 33(13Q21.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 33(13Q21.2) MUTATED   28 10
  DEL PEAK 33(13Q21.2) WILD-TYPE 39 21
  DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE 
                            38                             60 
  DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE 
                            10                             21 
$`DEL PEAK 33(13Q21.2) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         0.85        20.78         2.63         0.26         0.53 
TCGA-IG-A51D TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A4OE 
       17.03         0.13        44.75        60.39        53.85         3.52 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88V 
        3.68         6.41         4.08         3.16        29.00         2.60 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       83.24        10.36         0.07        10.45         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.13         0.07         0.07         0.13         0.07 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.10         0.10         0.07         0.20         7.59         5.06 
TCGA-R6-A6XQ TCGA-V5-A7RE 
        6.35         4.80 

$`DEL PEAK 33(13Q21.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 
       33.27        20.12         0.03         0.99         0.79         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        1.12         0.46       122.10         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
        6.21         3.16         3.45         0.30         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        3.35        19.50         8.78        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        1.38        30.74         4.90         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       16.47        21.37         0.16         0.10         0.10         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.10         0.07         0.07         0.10         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        5.16         3.78         8.02        14.70         7.04        29.59 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30         7.00         8.78        14.01         5.29 

  DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE 
                         2.895                          5.750 
[1] "0.1 - 83.2 (2.9)"  "0.0 - 122.1 (5.8)"
[1] "hr=" "1.1"
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(13Q21.2) MUTATED         2        2        1        1        13
  DEL PEAK 33(13Q21.2) WILD-TYPE       5        2        3        0        17
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(13Q21.2) MUTATED           7         5          4          2
  DEL PEAK 33(13Q21.2) WILD-TYPE         9         6          4          4
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 33(13Q21.2) MUTATED            1        0
  DEL PEAK 33(13Q21.2) WILD-TYPE          2        1
D59V3, multiclass
            clus
vv           DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE
  STAGE I                               2                              5
  STAGE IA                              2                              2
  STAGE IB                              1                              3
  STAGE II                              1                              0
  STAGE IIA                            13                             17
  STAGE IIB                             7                              9
  STAGE III                             5                              6
  STAGE IIIA                            4                              4
  STAGE IIIB                            2                              4
  STAGE IIIC                            1                              2
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 33(13Q21.2) MUTATED       7 11    20
  DEL PEAK 33(13Q21.2) WILD-TYPE    12 15    30
D59V4, multiclass
       clus
vv      DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE
  T0+T1                            7                             12
  T2                              11                             15
  T3+T4                           20                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 33(13Q21.2) MUTATED   22 13     3
  DEL PEAK 33(13Q21.2) WILD-TYPE 28 20     8
D59V5, multiclass
       clus
vv      DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE
  N0                              22                             28
  N1                              13                             20
  N2+N3                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 33(13Q21.2) MUTATED   32   0  3
  DEL PEAK 33(13Q21.2) WILD-TYPE 43   1 12
D59V6, multiclass
     clus
vv    DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE
  M0                            32                             43
  M1A                            0                              1
  MX                             3                             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                                cls
clus                              0  1
  DEL PEAK 33(13Q21.2) MUTATED    4 37
  DEL PEAK 33(13Q21.2) WILD-TYPE 11 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q21.2) MUTATED      4   37
  DEL PEAK 33(13Q21.2) WILD-TYPE   11   53
        clus
vv       DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE
  FEMALE                            4                             11
  MALE                             37                             53
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, binary
                                cls
clus                              0  1
  DEL PEAK 33(13Q21.2) MUTATED   20 21
  DEL PEAK 33(13Q21.2) WILD-TYPE 15 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q21.2) MUTATED     20   21
  DEL PEAK 33(13Q21.2) WILD-TYPE   15   45
       clus
vv      DEL PEAK 33(13Q21.2) MUTATED DEL PEAK 33(13Q21.2) WILD-TYPE
  ASIAN                           20                             15
  WHITE                           21                             45
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 34(14Q31.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 34(14Q31.1) MUTATED   22 12
  DEL PEAK 34(14Q31.1) WILD-TYPE 45 19
  DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE 
                            34                             64 
  DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE 
                            12                             19 
$`DEL PEAK 34(14Q31.1) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
       20.09         2.63         0.36         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A6FH TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        41.52        42.77         0.30         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW 
        3.68         3.35        19.50         3.16        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L 
        6.94         0.36         3.95        16.47        10.36        10.45 
TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.10         0.10        17.62         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
       29.59         6.35         9.30         7.00 

$`DEL PEAK 34(14Q31.1) WILD-TYPE`
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         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99         0.53        17.03         0.79         0.13         1.12 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J 
       53.85         3.68         6.21         3.16         3.45         4.31 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        8.78         6.41         4.08        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        1.38        30.74         4.90         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K 
       25.12         7.40         3.02        21.37        83.24         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.16         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.07         0.07         0.20         1.18 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        5.16         3.78         8.02        14.70         7.04        53.95 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        8.78        14.01         5.29         4.80 

  DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE 
                         7.065                          3.385 
[1] "0.1 - 122.1 (7.1)" "0.0 - 83.2 (3.4)" 
[1] "hr=" "1.3"
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(14Q31.1) MUTATED         4        1        1        0         5
  DEL PEAK 34(14Q31.1) WILD-TYPE       3        3        3        1        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(14Q31.1) MUTATED           6         6          1          3
  DEL PEAK 34(14Q31.1) WILD-TYPE        10         5          7          3
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 34(14Q31.1) MUTATED            1        0
  DEL PEAK 34(14Q31.1) WILD-TYPE          2        1
D60V3, multiclass
            clus
vv           DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE
  STAGE I                               4                              3
  STAGE IA                              1                              3
  STAGE IB                              1                              3
  STAGE II                              0                              1
  STAGE IIA                             5                             25
  STAGE IIB                             6                             10
  STAGE III                             6                              5
  STAGE IIIA                            1                              7
  STAGE IIIB                            3                              3
  STAGE IIIC                            1                              2
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 34(14Q31.1) MUTATED       8  6    17
  DEL PEAK 34(14Q31.1) WILD-TYPE    11 20    33
D60V4, multiclass
       clus
vv      DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE
  T0+T1                            8                             11
  T2                               6                             20
  T3+T4                           17                             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 34(14Q31.1) MUTATED   13 13     5
  DEL PEAK 34(14Q31.1) WILD-TYPE 37 20     6
D60V5, multiclass
       clus
vv      DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE
  N0                              13                             37
  N1                              13                             20
  N2+N3                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 34(14Q31.1) MUTATED   24   0  5
  DEL PEAK 34(14Q31.1) WILD-TYPE 51   1 10
D60V6, multiclass
     clus
vv    DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE
  M0                            24                             51
  M1A                            0                              1
  MX                             5                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                                cls
clus                              0  1
  DEL PEAK 34(14Q31.1) MUTATED    5 31
  DEL PEAK 34(14Q31.1) WILD-TYPE 10 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q31.1) MUTATED      5   31
  DEL PEAK 34(14Q31.1) WILD-TYPE   10   59
        clus
vv       DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE
  FEMALE                            5                             10
  MALE                             31                             59
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, binary
                                cls
clus                              0  1
  DEL PEAK 34(14Q31.1) MUTATED    9 24
  DEL PEAK 34(14Q31.1) WILD-TYPE 26 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q31.1) MUTATED      9   24
  DEL PEAK 34(14Q31.1) WILD-TYPE   26   42
       clus
vv      DEL PEAK 34(14Q31.1) MUTATED DEL PEAK 34(14Q31.1) WILD-TYPE
  ASIAN                            9                             26
  WHITE                           24                             42
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 35(15Q11.2) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 35(15Q11.2) MUTATED   20 11
  DEL PEAK 35(15Q11.2) WILD-TYPE 47 20
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            31                             67 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            11                             20 
$`DEL PEAK 35(15Q11.2) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A625 TCGA-L5-A43H TCGA-L5-A43M 
       20.09        20.12         0.26         0.36         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OT TCGA-L5-A4OU 
        3.52         3.35        19.50         4.08         4.90        29.00 
TCGA-L5-A893 TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A5 TCGA-LN-A4A8 
        3.02        83.24        10.45         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.10         0.20         1.18         5.16         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       14.70        29.59         9.30         7.00         8.78        14.01 
TCGA-V5-A7RE 
        4.80 

$`DEL PEAK 35(15Q11.2) WILD-TYPE`
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         0.03         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03         0.79         0.13         1.12         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        53.85         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF 
       42.77         6.21         3.16         3.45         4.31         3.68 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         6.41        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        3.16        30.74         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ 
        2.60        25.12         0.36         7.40         3.95        16.47 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       21.37        10.36         0.07         0.16         0.07         0.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.13         0.07         0.10         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.13         0.07         0.10         0.10         0.07         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
       17.62         3.78         8.02         7.04         6.35        53.95 
TCGA-V5-A7RB 
        5.29 

  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                          0.07                           0.03 
  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 
                          5.06                           3.68 
[1] "0.1 - 83.2 (5.1)"  "0.0 - 122.1 (3.7)"
[1] "hr=" "1.1"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(15Q11.2) MUTATED         3        1        2        0         7
  DEL PEAK 35(15Q11.2) WILD-TYPE       4        3        2        1        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(15Q11.2) MUTATED           3         4          2          4
  DEL PEAK 35(15Q11.2) WILD-TYPE        13         7          6          2
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 35(15Q11.2) MUTATED            0        1
  DEL PEAK 35(15Q11.2) WILD-TYPE          3        0
D61V3, multiclass
            clus
vv           DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  STAGE I                               3                              4
  STAGE IA                              1                              3
  STAGE IB                              2                              2
  STAGE II                              0                              1
  STAGE IIA                             7                             23
  STAGE IIB                             3                             13
  STAGE III                             4                              7
  STAGE IIIA                            2                              6
  STAGE IIIB                            4                              2
  STAGE IIIC                            0                              3
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 35(15Q11.2) MUTATED       6  7    15
  DEL PEAK 35(15Q11.2) WILD-TYPE    13 19    35
D61V4, multiclass
       clus
vv      DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  T0+T1                            6                             13
  T2                               7                             19
  T3+T4                           15                             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 35(15Q11.2) MUTATED   14  9     5
  DEL PEAK 35(15Q11.2) WILD-TYPE 36 24     6
D61V5, multiclass
       clus
vv      DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  N0                              14                             36
  N1                               9                             24
  N2+N3                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 35(15Q11.2) MUTATED   22   1  3
  DEL PEAK 35(15Q11.2) WILD-TYPE 53   0 12
D61V6, multiclass
     clus
vv    DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  M0                            22                             53
  M1A                            1                              0
  MX                             3                             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED    7 26
  DEL PEAK 35(15Q11.2) WILD-TYPE  8 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED      7   26
  DEL PEAK 35(15Q11.2) WILD-TYPE    8   64
        clus
vv       DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  FEMALE                            7                              8
  MALE                             26                             64
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED   10 22
  DEL PEAK 35(15Q11.2) WILD-TYPE 25 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED     10   22
  DEL PEAK 35(15Q11.2) WILD-TYPE   25   44
       clus
vv      DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  ASIAN                           10                             25
  WHITE                           22                             44
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 36(16Q23.1) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 36(16Q23.1) MUTATED   27 15
  DEL PEAK 36(16Q23.1) WILD-TYPE 40 16
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            42                             56 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            15                             16 
$`DEL PEAK 36(16Q23.1) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-JY-A6F8 TCGA-JY-A6FB 
       20.09        20.12         0.26         0.53       122.10        60.39 
TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ 
       42.77         3.16         8.94         3.52         3.68         6.41 
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        7.43         2.60         0.36         3.95         3.02        16.47 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49W 
       83.24        10.36        10.45         0.33         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.10         0.07         8.02         7.59         5.06        14.70 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        6.35        53.95         9.30         7.00         5.29         4.80 

$`DEL PEAK 36(16Q23.1) WILD-TYPE`
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         0.03         0.99 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79         0.36         0.13         1.12         0.46 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E 
       44.75        53.85         3.68        41.52         6.21         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM 
        0.30         4.31         3.35        19.50         8.78         4.08 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        3.32         7.17         1.38         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
        7.40        21.37         0.07         0.16         0.07         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.13         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 
        0.10         0.10         0.10         0.07         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L6 TCGA-R6-A6XG 
        1.18        17.62         5.16         3.78         7.04        29.59 
TCGA-S8-A6BV TCGA-S8-A6BW 
        8.78        14.01 

  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                        122.10                          53.85 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                         6.705                          2.975 
[1] "0.1 - 122.1 (6.7)" "0.0 - 53.9 (3.0)" 
[1] "hr=" "1.3"
D62V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(16Q23.1) MUTATED         4        1        1        0        10
  DEL PEAK 36(16Q23.1) WILD-TYPE       3        3        3        1        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(16Q23.1) MUTATED           8         5          2          2
  DEL PEAK 36(16Q23.1) WILD-TYPE         8         6          6          4
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 36(16Q23.1) MUTATED            1        1
  DEL PEAK 36(16Q23.1) WILD-TYPE          2        0
D62V3, multiclass
            clus
vv           DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  STAGE I                               4                              3
  STAGE IA                              1                              3
  STAGE IB                              1                              3
  STAGE II                              0                              1
  STAGE IIA                            10                             20
  STAGE IIB                             8                              8
  STAGE III                             5                              6
  STAGE IIIA                            2                              6
  STAGE IIIB                            2                              4
  STAGE IIIC                            1                              2
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 36(16Q23.1) MUTATED      11 10    18
  DEL PEAK 36(16Q23.1) WILD-TYPE     8 16    32
D62V4, multiclass
       clus
vv      DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  T0+T1                           11                              8
  T2                              10                             16
  T3+T4                           18                             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 36(16Q23.1) MUTATED   18 17     4
  DEL PEAK 36(16Q23.1) WILD-TYPE 32 16     7
D62V5, multiclass
       clus
vv      DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  N0                              18                             32
  N1                              17                             16
  N2+N3                            4                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 36(16Q23.1) MUTATED   29   1  6
  DEL PEAK 36(16Q23.1) WILD-TYPE 46   0  9
D62V6, multiclass
     clus
vv    DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  M0                            29                             46
  M1A                            1                              0
  MX                             6                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                                cls
clus                              0  1
  DEL PEAK 36(16Q23.1) MUTATED    7 40
  DEL PEAK 36(16Q23.1) WILD-TYPE  8 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED      7   40
  DEL PEAK 36(16Q23.1) WILD-TYPE    8   50
        clus
vv       DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  FEMALE                            7                              8
  MALE                             40                             50
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, binary
                                cls
clus                              0  1
  DEL PEAK 36(16Q23.1) MUTATED   12 32
  DEL PEAK 36(16Q23.1) WILD-TYPE 23 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     12   32
  DEL PEAK 36(16Q23.1) WILD-TYPE   23   34
       clus
vv      DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  ASIAN                           12                             23
  WHITE                           32                             34
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 37(17P11.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 37(17P11.2) MUTATED   28 15
  DEL PEAK 37(17P11.2) WILD-TYPE 39 16
  DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE 
                            43                             55 
  DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE 
                            15                             16 
$`DEL PEAK 37(17P11.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
        0.03         0.26         0.79       122.10        60.39        42.77 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        3.45         8.94         3.52         3.68         3.35        19.50 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         7.17         1.38         4.90        29.00         7.43 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L 
        2.60         3.95        16.47        83.24         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A8 TCGA-LN-A5U6 
        0.16         0.13         0.07         0.07         0.07         0.20 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
       17.62         5.16         3.78         7.59         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RE 
        4.80 

$`DEL PEAK 37(17P11.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99         0.53        17.03         0.36         0.13         1.12 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
        0.46        44.75        53.85         3.68        41.52         6.21 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16         0.30         4.31         8.78         6.41         4.08 
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T 
       18.35         3.16        30.74         7.13         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L7-A6VZ 
       25.12         0.36         7.40         3.02        21.37        10.36 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
        0.07         0.33         0.10         0.10         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XQ 
        0.10         0.07         1.18         8.02        14.70         6.35 
TCGA-V5-A7RB 
        5.29 

  DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE 
                        122.10                          53.85 
  DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE 
                          5.06                           3.16 
[1] "0.0 - 122.1 (5.1)" "0.1 - 53.9 (3.2)" 
[1] "hr=" "1.1"
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(17P11.2) MUTATED         5        1        3        0        12
  DEL PEAK 37(17P11.2) WILD-TYPE       2        3        1        1        18
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(17P11.2) MUTATED           6         3          2          4
  DEL PEAK 37(17P11.2) WILD-TYPE        10         8          6          2
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 37(17P11.2) MUTATED            1        1
  DEL PEAK 37(17P11.2) WILD-TYPE          2        0
D63V3, multiclass
            clus
vv           DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE
  STAGE I                               5                              2
  STAGE IA                              1                              3
  STAGE IB                              3                              1
  STAGE II                              0                              1
  STAGE IIA                            12                             18
  STAGE IIB                             6                             10
  STAGE III                             3                              8
  STAGE IIIA                            2                              6
  STAGE IIIB                            4                              2
  STAGE IIIC                            1                              2
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 37(17P11.2) MUTATED       9 12    19
  DEL PEAK 37(17P11.2) WILD-TYPE    10 14    31
D63V4, multiclass
       clus
vv      DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE
  T0+T1                            9                             10
  T2                              12                             14
  T3+T4                           19                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 37(17P11.2) MUTATED   21 12     7
  DEL PEAK 37(17P11.2) WILD-TYPE 29 21     4
D63V5, multiclass
       clus
vv      DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE
  N0                              21                             29
  N1                              12                             21
  N2+N3                            7                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 37(17P11.2) MUTATED   31   1  6
  DEL PEAK 37(17P11.2) WILD-TYPE 44   0  9
D63V6, multiclass
     clus
vv    DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE
  M0                            31                             44
  M1A                            1                              0
  MX                             6                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                                cls
clus                              0  1
  DEL PEAK 37(17P11.2) MUTATED    6 40
  DEL PEAK 37(17P11.2) WILD-TYPE  9 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(17P11.2) MUTATED      6   40
  DEL PEAK 37(17P11.2) WILD-TYPE    9   50
        clus
vv       DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE
  FEMALE                            6                              9
  MALE                             40                             50
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, binary
                                cls
clus                              0  1
  DEL PEAK 37(17P11.2) MUTATED   11 33
  DEL PEAK 37(17P11.2) WILD-TYPE 24 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(17P11.2) MUTATED     11   33
  DEL PEAK 37(17P11.2) WILD-TYPE   24   33
       clus
vv      DEL PEAK 37(17P11.2) MUTATED DEL PEAK 37(17P11.2) WILD-TYPE
  ASIAN                           11                             24
  WHITE                           33                             33
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 38(17Q25.3) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 38(17Q25.3) MUTATED   16  5
  DEL PEAK 38(17Q25.3) WILD-TYPE 51 26
  DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE 
                            21                             77 
  DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE 
                             5                             26 
$`DEL PEAK 38(17Q25.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR 
        0.03         0.79         3.35        19.50         6.41         3.16 
TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-LN-A49M TCGA-LN-A49S 
       29.00         0.36         7.40         3.95         0.16         0.13 
TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU 
        0.07         0.10         0.10         0.20         1.18         5.16 
TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-V5-A7RE 
        3.78         9.30         4.80 

$`DEL PEAK 38(17Q25.3) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.99         0.53        17.03         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        1.12         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI 
        0.30         4.31         8.94         3.52         3.68         8.78 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        4.08        18.35         3.32         7.17         1.38        30.74 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
       25.12         3.02        16.47        21.37        83.24        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
        0.07        10.45         0.07         0.33         0.10         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.07         0.10         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-R6-A6DN 
        0.10         0.07         0.07         0.07        17.62         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         7.00         8.78        14.01         5.29 

  DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE 
                          29.0                          122.1 
  DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE 
                          3.16                           5.29 
[1] "0.0 - 29.0 (3.2)"  "0.1 - 122.1 (5.3)"
[1] "hr=" "1.4"
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(17Q25.3) MUTATED         3        1        2        1         9
  DEL PEAK 38(17Q25.3) WILD-TYPE       4        3        2        0        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(17Q25.3) MUTATED           2         2          0          2
  DEL PEAK 38(17Q25.3) WILD-TYPE        14         9          8          4
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 38(17Q25.3) MUTATED            0        0
  DEL PEAK 38(17Q25.3) WILD-TYPE          3        1
D64V3, multiclass
            clus
vv           DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE
  STAGE I                               3                              4
  STAGE IA                              1                              3
  STAGE IB                              2                              2
  STAGE II                              1                              0
  STAGE IIA                             9                             21
  STAGE IIB                             2                             14
  STAGE III                             2                              9
  STAGE IIIA                            0                              8
  STAGE IIIB                            2                              4
  STAGE IIIC                            0                              3
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 38(17Q25.3) MUTATED       7  8     9
  DEL PEAK 38(17Q25.3) WILD-TYPE    12 18    41
D64V4, multiclass
       clus
vv      DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE
  T0+T1                            7                             12
  T2                               8                             18
  T3+T4                            9                             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 38(17Q25.3) MUTATED   16  6     2
  DEL PEAK 38(17Q25.3) WILD-TYPE 34 27     9
D64V5, multiclass
       clus
vv      DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE
  N0                              16                             34
  N1                               6                             27
  N2+N3                            2                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 38(17Q25.3) MUTATED   22   0  2
  DEL PEAK 38(17Q25.3) WILD-TYPE 53   1 13
D64V6, multiclass
     clus
vv    DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE
  M0                            22                             53
  M1A                            0                              1
  MX                             2                             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                                cls
clus                              0  1
  DEL PEAK 38(17Q25.3) MUTATED    4 21
  DEL PEAK 38(17Q25.3) WILD-TYPE 11 69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q25.3) MUTATED      4   21
  DEL PEAK 38(17Q25.3) WILD-TYPE   11   69
        clus
vv       DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE
  FEMALE                            4                             11
  MALE                             21                             69
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, binary
                                cls
clus                              0  1
  DEL PEAK 38(17Q25.3) MUTATED   11 14
  DEL PEAK 38(17Q25.3) WILD-TYPE 24 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q25.3) MUTATED     11   14
  DEL PEAK 38(17Q25.3) WILD-TYPE   24   52
       clus
vv      DEL PEAK 38(17Q25.3) MUTATED DEL PEAK 38(17Q25.3) WILD-TYPE
  ASIAN                           11                             24
  WHITE                           14                             52
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 39(18Q12.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 39(18Q12.2) MUTATED   34 18
  DEL PEAK 39(18Q12.2) WILD-TYPE 33 13
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                            52                             46 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                            18                             13 
$`DEL PEAK 39(18Q12.2) MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.85         2.63         0.26         0.53         0.79         0.13 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M 
       53.85         3.68        42.77         3.16         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP 
        3.52         3.68         3.35        19.50         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU 
        2.60         3.95         3.02        16.47        21.37        83.24 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36        10.45         0.16         0.07         0.33         0.10 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.07         0.07         0.10         0.10         0.10         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XQ 
       17.62         5.16         3.78         8.02         7.59         6.35 
TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       53.95         7.00         8.78         5.29 

$`DEL PEAK 39(18Q12.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       33.27        20.09        20.78        20.12         0.03         0.99 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
       17.03         0.36         1.12         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI 
       60.39        41.52         6.21         3.45         4.31         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A88T 
        6.41         4.08        18.35         1.38        30.74         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V 
       25.12         0.36         7.40         0.07         0.13         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 
        0.10         0.07         0.13         0.07         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.07         0.20         1.18         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-S8-A6BW TCGA-V5-A7RE 
       29.59         9.30        14.01         4.80 

  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                          3.73                           4.93 
[1] "0.1 - 83.2 (3.7)"  "0.0 - 122.1 (4.9)"
[1] "hr=" "1.4"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(18Q12.2) MUTATED         3        2        2        1        15
  DEL PEAK 39(18Q12.2) WILD-TYPE       4        2        2        0        15
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(18Q12.2) MUTATED           7         7          4          4
  DEL PEAK 39(18Q12.2) WILD-TYPE         9         4          4          2
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 39(18Q12.2) MUTATED            2        1
  DEL PEAK 39(18Q12.2) WILD-TYPE          1        0
D65V3, multiclass
            clus
vv           DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  STAGE I                               3                              4
  STAGE IA                              2                              2
  STAGE IB                              2                              2
  STAGE II                              1                              0
  STAGE IIA                            15                             15
  STAGE IIB                             7                              9
  STAGE III                             7                              4
  STAGE IIIA                            4                              4
  STAGE IIIB                            4                              2
  STAGE IIIC                            2                              1
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 39(18Q12.2) MUTATED       8 14    29
  DEL PEAK 39(18Q12.2) WILD-TYPE    11 12    21
D65V4, multiclass
       clus
vv      DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  T0+T1                            8                             11
  T2                              14                             12
  T3+T4                           29                             21
[1] 3 2
[1] 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(18Q12.2) MUTATED   24 20     7
  DEL PEAK 39(18Q12.2) WILD-TYPE 26 13     4
D65V5, multiclass
       clus
vv      DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  N0                              24                             26
  N1                              20                             13
  N2+N3                            7                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 39(18Q12.2) MUTATED   40   1  8
  DEL PEAK 39(18Q12.2) WILD-TYPE 35   0  7
D65V6, multiclass
     clus
vv    DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  M0                            40                             35
  M1A                            1                              0
  MX                             8                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                                cls
clus                              0  1
  DEL PEAK 39(18Q12.2) MUTATED    9 47
  DEL PEAK 39(18Q12.2) WILD-TYPE  6 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q12.2) MUTATED      9   47
  DEL PEAK 39(18Q12.2) WILD-TYPE    6   43
        clus
vv       DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  FEMALE                            9                              6
  MALE                             47                             43
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, binary
                                cls
clus                              0  1
  DEL PEAK 39(18Q12.2) MUTATED   17 35
  DEL PEAK 39(18Q12.2) WILD-TYPE 18 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q12.2) MUTATED     17   35
  DEL PEAK 39(18Q12.2) WILD-TYPE   18   31
       clus
vv      DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  ASIAN                           17                             18
  WHITE                           35                             31
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 40(18Q21.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 40(18Q21.2) MUTATED   39 19
  DEL PEAK 40(18Q21.2) WILD-TYPE 28 12
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                            58                             40 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                            19                             12 
$`DEL PEAK 40(18Q21.2) MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
        0.85         2.63         0.03         0.26         0.53         0.79 
TCGA-IG-A6QS TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43H 
        0.13        53.85         3.68        42.77         3.16         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        8.94         3.52         3.68         3.35        19.50         6.41 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         7.17         3.16         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ 
        6.94         2.60         3.95         3.02        16.47        21.37 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        10.36        10.45         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ 
        0.10         0.07         0.07         0.10         0.10         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.20         1.18        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         7.59        29.59         6.35        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        7.00         8.78         5.29         4.80 

$`DEL PEAK 40(18Q21.2) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D 
       33.27        20.09        20.78        20.12         0.99        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.36         1.12         0.46       122.10        44.75        60.39 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM 
       41.52         6.21         3.45         4.31         8.78         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W 
       18.35         1.38        30.74         7.13         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.36         7.40         0.07         0.13         0.07         0.10 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.10         0.13         0.07         0.10         0.07         0.07 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-S8-A6BW 
        5.06        14.70         7.04        14.01 

  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                         3.730                          5.635 
[1] "0.0 - 83.2 (3.7)"  "0.1 - 122.1 (5.6)"
[1] "hr=" "1.4"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(18Q21.2) MUTATED         4        2        3        1        15
  DEL PEAK 40(18Q21.2) WILD-TYPE       3        2        1        0        15
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18Q21.2) MUTATED           8         7          4          4
  DEL PEAK 40(18Q21.2) WILD-TYPE         8         4          4          2
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 40(18Q21.2) MUTATED            2        1
  DEL PEAK 40(18Q21.2) WILD-TYPE          1        0
D66V3, multiclass
            clus
vv           DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  STAGE I                               4                              3
  STAGE IA                              2                              2
  STAGE IB                              3                              1
  STAGE II                              1                              0
  STAGE IIA                            15                             15
  STAGE IIB                             8                              8
  STAGE III                             7                              4
  STAGE IIIA                            4                              4
  STAGE IIIB                            4                              2
  STAGE IIIC                            2                              1
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 40(18Q21.2) MUTATED      10 15    29
  DEL PEAK 40(18Q21.2) WILD-TYPE     9 11    21
D66V4, multiclass
       clus
vv      DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  T0+T1                           10                              9
  T2                              15                             11
  T3+T4                           29                             21
[1] 3 2
[1] 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(18Q21.2) MUTATED   26 21     7
  DEL PEAK 40(18Q21.2) WILD-TYPE 24 12     4
D66V5, multiclass
       clus
vv      DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  N0                              26                             24
  N1                              21                             12
  N2+N3                            7                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 40(18Q21.2) MUTATED   43   1  8
  DEL PEAK 40(18Q21.2) WILD-TYPE 32   0  7
D66V6, multiclass
     clus
vv    DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  M0                            43                             32
  M1A                            1                              0
  MX                             8                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                              0  1
  DEL PEAK 40(18Q21.2) MUTATED    9 52
  DEL PEAK 40(18Q21.2) WILD-TYPE  6 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q21.2) MUTATED      9   52
  DEL PEAK 40(18Q21.2) WILD-TYPE    6   38
        clus
vv       DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  FEMALE                            9                              6
  MALE                             52                             38
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, binary
                                cls
clus                              0  1
  DEL PEAK 40(18Q21.2) MUTATED   18 40
  DEL PEAK 40(18Q21.2) WILD-TYPE 17 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q21.2) MUTATED     18   40
  DEL PEAK 40(18Q21.2) WILD-TYPE   17   26
       clus
vv      DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  ASIAN                           18                             17
  WHITE                           40                             26
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 41(19P13.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 41(19P13.3) MUTATED   34  9
  DEL PEAK 41(19P13.3) WILD-TYPE 33 22
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            43                             55 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                             9                             22 
$`DEL PEAK 41(19P13.3) MUTATED`
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        2.63         0.03         0.26         0.53        17.03         0.79 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43E 
        0.46       122.10        44.75        53.85        42.77         3.45 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO 
        8.94         3.52         3.68        19.50         4.08         3.32 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
        7.17        30.74         7.43         2.60         0.36         3.95 
TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S 
       16.47        10.36        10.45         0.16         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.07         0.07         0.07         0.13         0.07         0.10 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        0.10         0.20         8.02         5.06         7.04        29.59 
TCGA-V5-A7RE 
        4.80 

$`DEL PEAK 41(19P13.3) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT 
       33.27        20.09         0.85        20.78        20.12         0.99 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
        0.36         0.13         1.12        60.39         3.68        41.52 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
        6.21         3.16         0.30         4.31         3.35         8.78 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        6.41        18.35         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        7.13         6.94         8.71        25.12         7.40         3.02 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49V 
       21.37        83.24         0.07         0.07         0.33         0.10 
TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.10         0.10         0.10         0.07         0.07         0.07 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 
        1.18        17.62         5.16         3.78         7.59        14.70 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB 
        5.29 

  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                          3.52                           5.29 
[1] "0.0 - 122.1 (3.5)" "0.1 - 83.2 (5.3)" 
[1] "hr=" "1.7"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(19P13.3) MUTATED         3        2        2        1        10
  DEL PEAK 41(19P13.3) WILD-TYPE       4        2        2        0        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(19P13.3) MUTATED           8         6          2          3
  DEL PEAK 41(19P13.3) WILD-TYPE         8         5          6          3
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 41(19P13.3) MUTATED            2        0
  DEL PEAK 41(19P13.3) WILD-TYPE          1        1
D67V3, multiclass
            clus
vv           DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  STAGE I                               3                              4
  STAGE IA                              2                              2
  STAGE IB                              2                              2
  STAGE II                              1                              0
  STAGE IIA                            10                             20
  STAGE IIB                             8                              8
  STAGE III                             6                              5
  STAGE IIIA                            2                              6
  STAGE IIIB                            3                              3
  STAGE IIIC                            2                              1
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 41(19P13.3) MUTATED       9 12    21
  DEL PEAK 41(19P13.3) WILD-TYPE    10 14    29
D67V4, multiclass
       clus
vv      DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  T0+T1                            9                             10
  T2                              12                             14
  T3+T4                           21                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 41(19P13.3) MUTATED   19 17     6
  DEL PEAK 41(19P13.3) WILD-TYPE 31 16     5
D67V5, multiclass
       clus
vv      DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  N0                              19                             31
  N1                              17                             16
  N2+N3                            6                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 41(19P13.3) MUTATED   34   0  5
  DEL PEAK 41(19P13.3) WILD-TYPE 41   1 10
D67V6, multiclass
     clus
vv    DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  M0                            34                             41
  M1A                            0                              1
  MX                             5                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                                cls
clus                              0  1
  DEL PEAK 41(19P13.3) MUTATED    5 41
  DEL PEAK 41(19P13.3) WILD-TYPE 10 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED      5   41
  DEL PEAK 41(19P13.3) WILD-TYPE   10   49
        clus
vv       DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  FEMALE                            5                             10
  MALE                             41                             49
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, binary
                                cls
clus                              0  1
  DEL PEAK 41(19P13.3) MUTATED   19 26
  DEL PEAK 41(19P13.3) WILD-TYPE 16 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED     19   26
  DEL PEAK 41(19P13.3) WILD-TYPE   16   40
       clus
vv      DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  ASIAN                           19                             16
  WHITE                           26                             40
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 42(19Q13.31) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 42(19Q13.31) MUTATED   19  4
  DEL PEAK 42(19Q13.31) WILD-TYPE 48 27
  DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE 
                             23                              75 
  DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE 
                              4                              27 
$`DEL PEAK 42(19Q13.31) MUTATED`
TCGA-IG-A3YB TCGA-IG-A50L TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43J 
        2.63         0.53        53.85        42.77         3.45         4.31 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 
        4.08         7.17        30.74         7.43         6.94         3.95 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       10.45         0.16         0.10         0.13         0.10         0.07 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-R6-A6DN 
        0.07         0.13         0.10         0.20         8.02 

$`DEL PEAK 42(19Q13.31) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.99        17.03         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
        1.12         0.46       122.10        44.75        60.39         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
       41.52         6.21         3.16         0.30         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        3.68         3.35        19.50         8.78         6.41        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         1.38         3.16         4.90        29.00         7.13 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
        8.71         2.60        25.12         0.36         7.40         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       16.47        21.37        83.24        10.36         0.07         0.07 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.33         0.07         0.10         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.07         0.10         0.07         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         3.78         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
       29.59         6.35        53.95         9.30         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       14.01         5.29         4.80 

  DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE 
                          53.85                          122.10 
  DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE 
                           3.45                            5.06 
[1] "0.1 - 53.9 (3.5)"  "0.0 - 122.1 (5.1)"
[1] "hr=" "1.5"
D68V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(19Q13.31) MUTATED         1        2        1        1        11
  DEL PEAK 42(19Q13.31) WILD-TYPE       6        2        3        0        19
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(19Q13.31) MUTATED           5         3          2          0
  DEL PEAK 42(19Q13.31) WILD-TYPE        11         8          6          6
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 42(19Q13.31) MUTATED            0        0
  DEL PEAK 42(19Q13.31) WILD-TYPE          3        1
D68V3, multiclass
            clus
vv           DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE
  STAGE I                                1                               6
  STAGE IA                               2                               2
  STAGE IB                               1                               3
  STAGE II                               1                               0
  STAGE IIA                             11                              19
  STAGE IIB                              5                              11
  STAGE III                              3                               8
  STAGE IIIA                             2                               6
  STAGE IIIB                             0                               6
  STAGE IIIC                             0                               3
  STAGE IV                               0                               1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3+T4
  DEL PEAK 42(19Q13.31) MUTATED       3  9    15
  DEL PEAK 42(19Q13.31) WILD-TYPE    16 17    35
D68V4, multiclass
       clus
vv      DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE
  T0+T1                             3                              16
  T2                                9                              17
  T3+T4                            15                              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 42(19Q13.31) MUTATED   17 10     0
  DEL PEAK 42(19Q13.31) WILD-TYPE 33 23    11
D68V5, multiclass
       clus
vv      DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE
  N0                               17                              33
  N1                               10                              23
  N2+N3                             0                              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1A MX
  DEL PEAK 42(19Q13.31) MUTATED   23   0  3
  DEL PEAK 42(19Q13.31) WILD-TYPE 52   1 12
D68V6, multiclass
     clus
vv    DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE
  M0                             23                              52
  M1A                             0                               1
  MX                              3                              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                                 cls
clus                               0  1
  DEL PEAK 42(19Q13.31) MUTATED    4 24
  DEL PEAK 42(19Q13.31) WILD-TYPE 11 66
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.31) MUTATED      4   24
  DEL PEAK 42(19Q13.31) WILD-TYPE   11   66
        clus
vv       DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE
  FEMALE                             4                              11
  MALE                              24                              66
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, binary
                                 cls
clus                               0  1
  DEL PEAK 42(19Q13.31) MUTATED   17 11
  DEL PEAK 42(19Q13.31) WILD-TYPE 18 55
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.31) MUTATED     17   11
  DEL PEAK 42(19Q13.31) WILD-TYPE   18   55
       clus
vv      DEL PEAK 42(19Q13.31) MUTATED DEL PEAK 42(19Q13.31) WILD-TYPE
  ASIAN                            17                              18
  WHITE                            11                              55
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 43(20P12.1) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 43(20P12.1) MUTATED   14  5
  DEL PEAK 43(20P12.1) WILD-TYPE 53 26
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                            19                             79 
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                             5                             26 
$`DEL PEAK 43(20P12.1) MUTATED`
TCGA-IG-A4QS TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OF 
        0.26        44.75        53.85        42.77         8.94         3.68 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L 
       19.50         3.32        16.47        83.24        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49Y TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6Y0 
        0.16         0.33         0.07         5.06        29.59        53.95 
TCGA-S8-A6BW 
       14.01 

$`DEL PEAK 43(20P12.1) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         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 
        0.03         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE 
        0.13         1.12         0.46       122.10        60.39         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       41.52         6.21         3.16         3.45         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.52         3.35         8.78         6.41         4.08        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-LN-A49K 
        0.36         7.40         3.95         3.02        21.37         0.07 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        0.07         0.10         0.13         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.07         0.07         0.10         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       17.62         5.16         3.78         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        7.04         6.35         9.30         7.00         8.78         5.29 
TCGA-V5-A7RE 
        4.80 

  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                         10.45                           3.68 
[1] "0.1 - 83.2 (10.4)" "0.0 - 122.1 (3.7)"
[1] "hr=" "2.6"
D69V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(20P12.1) MUTATED         1        0        1        0         7
  DEL PEAK 43(20P12.1) WILD-TYPE       6        4        3        1        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(20P12.1) MUTATED           3         2          0          1
  DEL PEAK 43(20P12.1) WILD-TYPE        13         9          8          5
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 43(20P12.1) MUTATED            2        0
  DEL PEAK 43(20P12.1) WILD-TYPE          1        1
D69V3, multiclass
            clus
vv           DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  STAGE I                               1                              6
  STAGE IA                              0                              4
  STAGE IB                              1                              3
  STAGE II                              0                              1
  STAGE IIA                             7                             23
  STAGE IIB                             3                             13
  STAGE III                             2                              9
  STAGE IIIA                            0                              8
  STAGE IIIB                            1                              5
  STAGE IIIC                            2                              1
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 43(20P12.1) MUTATED       2  7     9
  DEL PEAK 43(20P12.1) WILD-TYPE    17 19    41
D69V4, multiclass
       clus
vv      DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  T0+T1                            2                             17
  T2                               7                             19
  T3+T4                            9                             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 43(20P12.1) MUTATED    9  5     4
  DEL PEAK 43(20P12.1) WILD-TYPE 41 28     7
D69V5, multiclass
       clus
vv      DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  N0                               9                             41
  N1                               5                             28
  N2+N3                            4                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 43(20P12.1) MUTATED   14   0  3
  DEL PEAK 43(20P12.1) WILD-TYPE 61   1 12
D69V6, multiclass
     clus
vv    DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  M0                            14                             61
  M1A                            0                              1
  MX                             3                             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                                cls
clus                              0  1
  DEL PEAK 43(20P12.1) MUTATED    2 19
  DEL PEAK 43(20P12.1) WILD-TYPE 13 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(20P12.1) MUTATED      2   19
  DEL PEAK 43(20P12.1) WILD-TYPE   13   71
        clus
vv       DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  FEMALE                            2                             13
  MALE                             19                             71
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, binary
                                cls
clus                              0  1
  DEL PEAK 43(20P12.1) MUTATED    8 12
  DEL PEAK 43(20P12.1) WILD-TYPE 27 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(20P12.1) MUTATED      8   12
  DEL PEAK 43(20P12.1) WILD-TYPE   27   54
       clus
vv      DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  ASIAN                            8                             27
  WHITE                           12                             54
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 44(21Q11.2) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 44(21Q11.2) MUTATED   43 16
  DEL PEAK 44(21Q11.2) WILD-TYPE 24 15
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                            59                             39 
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                            16                             15 
$`DEL PEAK 44(21Q11.2) MUTATED`
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         0.03         0.26 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43C 
        0.53         0.79         0.13       122.10        53.85         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.45         0.30         4.31         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
        3.35        19.50         4.08        18.35         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       30.74         4.90        29.00         7.13         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L7-A6VZ 
        0.36         7.40         3.95         3.02        16.47        10.36 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W 
        0.07         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.10         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 
        0.20        17.62         3.78         8.02         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-S8-A6BW TCGA-V5-A7RE 
       29.59         6.35         9.30        14.01         4.80 

$`DEL PEAK 44(21Q11.2) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP 
       20.09         2.63         0.99        17.03         0.36         1.12 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        0.46        44.75        60.39         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX 
        6.21         8.78         6.41         3.32         1.38         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
        8.71        25.12        21.37        83.24        10.45         0.16 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A8 
        0.07         0.10         0.07         0.13         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y0 
        0.10         1.18         5.16         7.59        14.70        53.95 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        7.00         8.78         5.29 

  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                          3.78                           6.21 
[1] "0.0 - 122.1 (3.8)" "0.1 - 83.2 (6.2)" 
[1] "hr=" "1.1"
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(21Q11.2) MUTATED         5        3        4        1        15
  DEL PEAK 44(21Q11.2) WILD-TYPE       2        1        0        0        15
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(21Q11.2) MUTATED           9         7          4          3
  DEL PEAK 44(21Q11.2) WILD-TYPE         7         4          4          3
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 44(21Q11.2) MUTATED            1        1
  DEL PEAK 44(21Q11.2) WILD-TYPE          2        0
D70V3, multiclass
            clus
vv           DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  STAGE I                               5                              2
  STAGE IA                              3                              1
  STAGE IB                              4                              0
  STAGE II                              1                              0
  STAGE IIA                            15                             15
  STAGE IIB                             9                              7
  STAGE III                             7                              4
  STAGE IIIA                            4                              4
  STAGE IIIB                            3                              3
  STAGE IIIC                            1                              2
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 44(21Q11.2) MUTATED      13 14    29
  DEL PEAK 44(21Q11.2) WILD-TYPE     6 12    21
D70V4, multiclass
       clus
vv      DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  T0+T1                           13                              6
  T2                              14                             12
  T3+T4                           29                             21
[1] 3 2
[1] 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(21Q11.2) MUTATED   31 20     5
  DEL PEAK 44(21Q11.2) WILD-TYPE 19 13     6
D70V5, multiclass
       clus
vv      DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  N0                              31                             19
  N1                              20                             13
  N2+N3                            5                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 44(21Q11.2) MUTATED   42   1  9
  DEL PEAK 44(21Q11.2) WILD-TYPE 33   0  6
D70V6, multiclass
     clus
vv    DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  M0                            42                             33
  M1A                            1                              0
  MX                             9                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                                cls
clus                              0  1
  DEL PEAK 44(21Q11.2) MUTATED   10 53
  DEL PEAK 44(21Q11.2) WILD-TYPE  5 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(21Q11.2) MUTATED     10   53
  DEL PEAK 44(21Q11.2) WILD-TYPE    5   37
        clus
vv       DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  FEMALE                           10                              5
  MALE                             53                             37
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, binary
                                cls
clus                              0  1
  DEL PEAK 44(21Q11.2) MUTATED   19 41
  DEL PEAK 44(21Q11.2) WILD-TYPE 16 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(21Q11.2) MUTATED     19   41
  DEL PEAK 44(21Q11.2) WILD-TYPE   16   25
       clus
vv      DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  ASIAN                           19                             16
  WHITE                           41                             25
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 45(21Q22.12) MUTATION ANALYSIS
D71V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 45(21Q22.12) MUTATED   39 18
  DEL PEAK 45(21Q22.12) WILD-TYPE 28 13
  DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE 
                             57                              41 
  DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE 
                             18                              13 
$`DEL PEAK 45(21Q22.12) MUTATED`
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         0.03         0.26 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FH 
        0.53         0.79         0.13       122.10        44.75        42.77 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        3.16         3.45         0.30         4.31         8.94         3.52 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
        3.35        19.50         6.41         4.08         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       30.74         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        2.60         0.36         7.40         3.95         3.02        16.47 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49X 
       10.36         0.07         0.07         0.33         0.13         0.10 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 
        0.07         0.10         0.10         0.07         0.20        17.62 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        3.78         8.02         7.59         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-V5-A7RE 
        6.35         9.30         4.80 

$`DEL PEAK 45(21Q22.12) WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP 
       20.09         2.63         0.99        17.03         0.36         1.12 
TCGA-IG-A8O2 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
        0.46        60.39        53.85         3.68        41.52         6.21 
TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88T 
        3.68         8.78        18.35         3.32         1.38         8.71 
TCGA-L5-A88W TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       25.12        21.37        83.24        10.45         0.16         0.10 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.07         0.13         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6L4 
        0.10         0.07         0.07         1.18         5.16        14.70 
TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         7.00         8.78        14.01         5.29 

  DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE 
                           0.03                            0.07 
  DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE 
                         122.10                           83.24 
  DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE 
                           4.31                            3.68 
[1] "0.0 - 122.1 (4.3)" "0.1 - 83.2 (3.7)" 
[1] "hr=" "1.1"
D71V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(21Q22.12) MUTATED         6        3        3        1        12
  DEL PEAK 45(21Q22.12) WILD-TYPE       1        1        1        0        18
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(21Q22.12) MUTATED          10         6          4          3
  DEL PEAK 45(21Q22.12) WILD-TYPE         6         5          4          3
                                 vv
clus                              STAGE IIIC STAGE IV
  DEL PEAK 45(21Q22.12) MUTATED            1        1
  DEL PEAK 45(21Q22.12) WILD-TYPE          2        0
D71V3, multiclass
            clus
vv           DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE
  STAGE I                                6                               1
  STAGE IA                               3                               1
  STAGE IB                               3                               1
  STAGE II                               1                               0
  STAGE IIA                             12                              18
  STAGE IIB                             10                               6
  STAGE III                              6                               5
  STAGE IIIA                             4                               4
  STAGE IIIB                             3                               3
  STAGE IIIC                             1                               2
  STAGE IV                               1                               0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3+T4
  DEL PEAK 45(21Q22.12) MUTATED      12 14    27
  DEL PEAK 45(21Q22.12) WILD-TYPE     7 12    23
D71V4, multiclass
       clus
vv      DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE
  T0+T1                            12                               7
  T2                               14                              12
  T3+T4                            27                              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 45(21Q22.12) MUTATED   28 20     5
  DEL PEAK 45(21Q22.12) WILD-TYPE 22 13     6
D71V5, multiclass
       clus
vv      DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE
  N0                               28                              22
  N1                               20                              13
  N2+N3                             5                               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1A MX
  DEL PEAK 45(21Q22.12) MUTATED   42   1  8
  DEL PEAK 45(21Q22.12) WILD-TYPE 33   0  7
D71V6, multiclass
     clus
vv    DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE
  M0                             42                              33
  M1A                             1                               0
  MX                              8                               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                                 cls
clus                               0  1
  DEL PEAK 45(21Q22.12) MUTATED   11 50
  DEL PEAK 45(21Q22.12) WILD-TYPE  4 40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(21Q22.12) MUTATED     11   50
  DEL PEAK 45(21Q22.12) WILD-TYPE    4   40
        clus
vv       DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE
  FEMALE                            11                               4
  MALE                              50                              40
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, binary
                                 cls
clus                               0  1
  DEL PEAK 45(21Q22.12) MUTATED   16 42
  DEL PEAK 45(21Q22.12) WILD-TYPE 19 24
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(21Q22.12) MUTATED     16   42
  DEL PEAK 45(21Q22.12) WILD-TYPE   19   24
       clus
vv      DEL PEAK 45(21Q22.12) MUTATED DEL PEAK 45(21Q22.12) WILD-TYPE
  ASIAN                            16                              19
  WHITE                            42                              24
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 46(22Q11.1) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 46(22Q11.1) MUTATED   25 14
  DEL PEAK 46(22Q11.1) WILD-TYPE 42 17
  DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE 
                            39                             59 
  DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE 
                            14                             17 
$`DEL PEAK 46(22Q11.1) MUTATED`
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-JY-A6F8 
        2.63         0.03         0.26         0.53         0.79       122.10 
TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4ON 
       42.77         3.16         3.52         3.35        19.50        18.35 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        2.60         0.36         7.40         3.95         3.02        16.47 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.36         0.07        10.45         0.33         0.10         0.07 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.10         0.07         8.02         7.59         5.06 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        7.00         5.29         4.80 

$`DEL PEAK 46(22Q11.1) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT 
       33.27        20.09         0.85        20.78        20.12         0.99 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA 
       17.03         0.36         0.13         1.12         0.46        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E 
       60.39        53.85         3.68        41.52         6.21         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ 
        0.30         4.31         8.94         3.68         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.08         3.32         1.38         7.43         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S 
       25.12        21.37        83.24         0.16         0.07         0.13 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10         0.07         0.13         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.07         0.07         0.10         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       17.62         5.16         3.78        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30         8.78        14.01 

  DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE 
                          3.95                           4.31 
[1] "0.0 - 122.1 (4.0)" "0.1 - 83.2 (4.3)" 
[1] "hr=" "1.5"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(22Q11.1) MUTATED         4        2        2        0         9
  DEL PEAK 46(22Q11.1) WILD-TYPE       3        2        2        1        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(22Q11.1) MUTATED           6         6          2          2
  DEL PEAK 46(22Q11.1) WILD-TYPE        10         5          6          4
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 46(22Q11.1) MUTATED            1        1
  DEL PEAK 46(22Q11.1) WILD-TYPE          2        0
D72V3, multiclass
            clus
vv           DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE
  STAGE I                               4                              3
  STAGE IA                              2                              2
  STAGE IB                              2                              2
  STAGE II                              0                              1
  STAGE IIA                             9                             21
  STAGE IIB                             6                             10
  STAGE III                             6                              5
  STAGE IIIA                            2                              6
  STAGE IIIB                            2                              4
  STAGE IIIC                            1                              2
  STAGE IV                              1                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 46(22Q11.1) MUTATED      12  7    19
  DEL PEAK 46(22Q11.1) WILD-TYPE     7 19    31
D72V4, multiclass
       clus
vv      DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE
  T0+T1                           12                              7
  T2                               7                             19
  T3+T4                           19                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 46(22Q11.1) MUTATED   17 18     3
  DEL PEAK 46(22Q11.1) WILD-TYPE 33 15     8
D72V5, multiclass
       clus
vv      DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE
  N0                              17                             33
  N1                              18                             15
  N2+N3                            3                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 46(22Q11.1) MUTATED   29   1  6
  DEL PEAK 46(22Q11.1) WILD-TYPE 46   0  9
D72V6, multiclass
     clus
vv    DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE
  M0                            29                             46
  M1A                            1                              0
  MX                             6                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                                cls
clus                              0  1
  DEL PEAK 46(22Q11.1) MUTATED    8 34
  DEL PEAK 46(22Q11.1) WILD-TYPE  7 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(22Q11.1) MUTATED      8   34
  DEL PEAK 46(22Q11.1) WILD-TYPE    7   56
        clus
vv       DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE
  FEMALE                            8                              7
  MALE                             34                             56
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, binary
                                cls
clus                              0  1
  DEL PEAK 46(22Q11.1) MUTATED   12 28
  DEL PEAK 46(22Q11.1) WILD-TYPE 23 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(22Q11.1) MUTATED     12   28
  DEL PEAK 46(22Q11.1) WILD-TYPE   23   38
       clus
vv      DEL PEAK 46(22Q11.1) MUTATED DEL PEAK 46(22Q11.1) WILD-TYPE
  ASIAN                           12                             23
  WHITE                           28                             38
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 47(XP21.1) MUTATION ANALYSIS
D73V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 47(XP21.1) MUTATED   25 11
  DEL PEAK 47(XP21.1) WILD-TYPE 42 20
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                           36                            62 
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                           11                            20 
$`DEL PEAK 47(XP21.1) MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L 
       33.27        20.09         0.85        20.78         0.26         0.53 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FH 
       17.03         0.36         0.13         0.46        44.75        42.77 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.31         3.52         3.68         6.41         4.08        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A891 TCGA-L5-A8NJ TCGA-LN-A49K TCGA-LN-A49M 
        7.17         1.38         3.95        16.47         0.07         0.16 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.07         0.13         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-S8-A6BV TCGA-V5-A7RB 
        1.18        17.62         5.16         8.02         8.78         5.29 

$`DEL PEAK 47(XP21.1) WILD-TYPE`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP 
        2.63        20.12         0.03         0.99         0.79         1.12 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
      122.10        60.39        53.85         3.68        41.52         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH 
        3.16         3.45         0.30         8.94         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        8.78         3.32         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        0.36         7.40         3.02        21.37        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45         0.07         0.33         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.07         0.10         0.07         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.07         0.10         3.78         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.04        29.59         6.35        53.95         9.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE 
       14.01         4.80 

  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                        44.75                        122.10 
  DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE 
                        3.815                         4.980 
[1] "0.1 - 44.8 (3.8)"  "0.0 - 122.1 (5.0)"
[1] "hr=" "1.2"
D73V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(XP21.1) MUTATED         1        2        0        0        14
  DEL PEAK 47(XP21.1) WILD-TYPE       6        2        4        1        16
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(XP21.1) MUTATED           9         2          5          5
  DEL PEAK 47(XP21.1) WILD-TYPE         7         9          3          1
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 47(XP21.1) MUTATED            0        0
  DEL PEAK 47(XP21.1) WILD-TYPE          3        1
D73V3, multiclass
            clus
vv           DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  STAGE I                              1                             6
  STAGE IA                             2                             2
  STAGE IB                             0                             4
  STAGE II                             0                             1
  STAGE IIA                           14                            16
  STAGE IIB                            9                             7
  STAGE III                            2                             9
  STAGE IIIA                           5                             3
  STAGE IIIB                           5                             1
  STAGE IIIC                           0                             3
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 47(XP21.1) MUTATED       7 12    21
  DEL PEAK 47(XP21.1) WILD-TYPE    12 14    29
D73V4, multiclass
       clus
vv      DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  T0+T1                           7                            12
  T2                             12                            14
  T3+T4                          21                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 47(XP21.1) MUTATED   21 13     6
  DEL PEAK 47(XP21.1) WILD-TYPE 29 20     5
D73V5, multiclass
       clus
vv      DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  N0                             21                            29
  N1                             13                            20
  N2+N3                           6                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 47(XP21.1) MUTATED   31   0  5
  DEL PEAK 47(XP21.1) WILD-TYPE 44   1 10
D73V6, multiclass
     clus
vv    DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  M0                           31                            44
  M1A                           0                             1
  MX                            5                            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                               cls
clus                             0  1
  DEL PEAK 47(XP21.1) MUTATED    5 36
  DEL PEAK 47(XP21.1) WILD-TYPE 10 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.1) MUTATED      5   36
  DEL PEAK 47(XP21.1) WILD-TYPE   10   54
        clus
vv       DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  FEMALE                           5                            10
  MALE                            36                            54
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, binary
                               cls
clus                             0  1
  DEL PEAK 47(XP21.1) MUTATED   18 21
  DEL PEAK 47(XP21.1) WILD-TYPE 17 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.1) MUTATED     18   21
  DEL PEAK 47(XP21.1) WILD-TYPE   17   45
       clus
vv      DEL PEAK 47(XP21.1) MUTATED DEL PEAK 47(XP21.1) WILD-TYPE
  ASIAN                          18                            17
  WHITE                          21                            45
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 48(XP11.3) MUTATION ANALYSIS
D74V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 48(XP11.3) MUTATED   27  9
  DEL PEAK 48(XP11.3) WILD-TYPE 40 22
  DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE 
                           36                            62 
  DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE 
                            9                            22 
$`DEL PEAK 48(XP11.3) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         0.85        20.78        20.12         0.26         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA 
       17.03         0.79         0.36         0.13         0.46        44.75 
TCGA-JY-A6FH TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
       42.77         4.31         3.52         3.68         6.41         4.08 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NJ TCGA-LN-A49K TCGA-LN-A49M 
       18.35         7.17         3.95        16.47         0.07         0.16 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 
        0.10         0.07         0.10         0.07         0.13         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-S8-A6BV 
        0.07         0.07         1.18        17.62         5.16         8.78 

$`DEL PEAK 48(XP11.3) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6F8 
       33.27         2.63         0.03         0.99         1.12       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C 
       60.39        53.85         3.68        41.52         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        3.45         0.30         8.94         3.35        19.50         8.78 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        0.36         7.40         3.02        21.37        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45         0.07         0.33         0.13         0.07         0.10 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 
        0.07         0.10         0.10         0.07         0.10         0.20 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        3.78         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW 
       29.59         6.35        53.95         9.30         7.00        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE 
                        44.75                        122.10 
  DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE 
                         2.35                          5.75 
[1] "0.1 - 44.8 (2.4)"  "0.0 - 122.1 (5.8)"
[1] "hr=" "1.1"
D74V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(XP11.3) MUTATED         1        2        1        0        16
  DEL PEAK 48(XP11.3) WILD-TYPE       6        2        3        1        14
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(XP11.3) MUTATED           8         4          5          5
  DEL PEAK 48(XP11.3) WILD-TYPE         8         7          3          1
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK 48(XP11.3) MUTATED            0        0
  DEL PEAK 48(XP11.3) WILD-TYPE          3        1
D74V3, multiclass
            clus
vv           DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE
  STAGE I                              1                             6
  STAGE IA                             2                             2
  STAGE IB                             1                             3
  STAGE II                             0                             1
  STAGE IIA                           16                            14
  STAGE IIB                            8                             8
  STAGE III                            4                             7
  STAGE IIIA                           5                             3
  STAGE IIIB                           5                             1
  STAGE IIIC                           0                             3
  STAGE IV                             0                             1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3+T4
  DEL PEAK 48(XP11.3) MUTATED       6 12    25
  DEL PEAK 48(XP11.3) WILD-TYPE    13 14    25
D74V4, multiclass
       clus
vv      DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE
  T0+T1                           6                            13
  T2                             12                            14
  T3+T4                          25                            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 48(XP11.3) MUTATED   24 14     5
  DEL PEAK 48(XP11.3) WILD-TYPE 26 19     6
D74V5, multiclass
       clus
vv      DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE
  N0                             24                            26
  N1                             14                            19
  N2+N3                           5                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1A MX
  DEL PEAK 48(XP11.3) MUTATED   36   0  3
  DEL PEAK 48(XP11.3) WILD-TYPE 39   1 12
D74V6, multiclass
     clus
vv    DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE
  M0                           36                            39
  M1A                           0                             1
  MX                            3                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                               cls
clus                             0  1
  DEL PEAK 48(XP11.3) MUTATED    4 39
  DEL PEAK 48(XP11.3) WILD-TYPE 11 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 48(XP11.3) MUTATED      4   39
  DEL PEAK 48(XP11.3) WILD-TYPE   11   51
        clus
vv       DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE
  FEMALE                           4                            11
  MALE                            39                            51
[1] 2 2
[1] FALSE
D74V8, continuous
D74V9, binary
                               cls
clus                             0  1
  DEL PEAK 48(XP11.3) MUTATED   22 20
  DEL PEAK 48(XP11.3) WILD-TYPE 13 46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 48(XP11.3) MUTATED     22   20
  DEL PEAK 48(XP11.3) WILD-TYPE   13   46
       clus
vv      DEL PEAK 48(XP11.3) MUTATED DEL PEAK 48(XP11.3) WILD-TYPE
  ASIAN                          22                            13
  WHITE                          20                            46
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 49(XQ21.33) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 49(XQ21.33) MUTATED   18  3
  DEL PEAK 49(XQ21.33) WILD-TYPE 49 28
  DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE 
                            21                             77 
  DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE 
                             3                             28 
$`DEL PEAK 49(XQ21.33) MUTATED`
TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
       42.77         8.94         6.41         4.08         7.17         3.16 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NJ TCGA-LN-A49M TCGA-LN-A49W TCGA-LN-A49Y 
        0.36         3.95        16.47         0.16         0.07         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.13         0.10         0.10         0.07         1.18        17.62 
TCGA-R6-A6KZ TCGA-RE-A7BO TCGA-V5-A7RE 
        5.06         7.00         4.80 

$`DEL PEAK 49(XQ21.33) WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        0.03         0.26         0.99         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.36         0.13         1.12         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C 
       60.39        53.85         3.68        41.52         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.45         0.30         4.31         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
       19.50         8.78        18.35         3.32         1.38        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU 
        2.60        25.12         7.40         3.02        21.37        83.24 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36         0.07        10.45         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.13         0.07         0.10         0.10         0.07         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.10         0.07         0.20         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30         8.78        14.01         5.29 

  DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE 
                         42.77                         122.10 
  DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE 
                          3.95                           4.90 
[1] "0.1 - 42.8 (4.0)"  "0.0 - 122.1 (4.9)"
[1] "hr=" "1.6"
D75V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(XQ21.33) MUTATED         1        3        1        1         8
  DEL PEAK 49(XQ21.33) WILD-TYPE       6        1        3        0        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(XQ21.33) MUTATED           2         3          0          0
  DEL PEAK 49(XQ21.33) WILD-TYPE        14         8          8          6
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 49(XQ21.33) MUTATED            0        0
  DEL PEAK 49(XQ21.33) WILD-TYPE          3        1
D75V3, multiclass
            clus
vv           DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE
  STAGE I                               1                              6
  STAGE IA                              3                              1
  STAGE IB                              1                              3
  STAGE II                              1                              0
  STAGE IIA                             8                             22
  STAGE IIB                             2                             14
  STAGE III                             3                              8
  STAGE IIIA                            0                              8
  STAGE IIIB                            0                              6
  STAGE IIIC                            0                              3
  STAGE IV                              0                              1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3+T4
  DEL PEAK 49(XQ21.33) MUTATED       7  7     8
  DEL PEAK 49(XQ21.33) WILD-TYPE    12 19    42
D75V4, multiclass
       clus
vv      DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE
  T0+T1                            7                             12
  T2                               7                             19
  T3+T4                            8                             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 49(XQ21.33) MUTATED   15  6     1
  DEL PEAK 49(XQ21.33) WILD-TYPE 35 27    10
D75V5, multiclass
       clus
vv      DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE
  N0                              15                             35
  N1                               6                             27
  N2+N3                            1                             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1A MX
  DEL PEAK 49(XQ21.33) MUTATED   17   0  4
  DEL PEAK 49(XQ21.33) WILD-TYPE 58   1 11
D75V6, multiclass
     clus
vv    DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE
  M0                            17                             58
  M1A                            0                              1
  MX                             4                             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                                cls
clus                              0  1
  DEL PEAK 49(XQ21.33) MUTATED    5 18
  DEL PEAK 49(XQ21.33) WILD-TYPE 10 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(XQ21.33) MUTATED      5   18
  DEL PEAK 49(XQ21.33) WILD-TYPE   10   72
        clus
vv       DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE
  FEMALE                            5                             10
  MALE                             18                             72
[1] 2 2
[1] FALSE
D75V8, continuous
D75V9, binary
                                cls
clus                              0  1
  DEL PEAK 49(XQ21.33) MUTATED   10 11
  DEL PEAK 49(XQ21.33) WILD-TYPE 25 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(XQ21.33) MUTATED     10   11
  DEL PEAK 49(XQ21.33) WILD-TYPE   25   55
       clus
vv      DEL PEAK 49(XQ21.33) MUTATED DEL PEAK 49(XQ21.33) WILD-TYPE
  ASIAN                           10                             25
  WHITE                           11                             55
[1] 2 2
[1] FALSE
