[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/11541396/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/11548800/transformed.cor.cli.txt"

nPatients in clinical file=151, in cluster file=184, common to both=150
[1]  85 150
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           30                           120 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           30                           120 
[1] "AMP PEAK  2(1Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           72                            78 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           72                            78 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           75                            75 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           75                            75 
[1] "AMP PEAK  4(2Q14.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           43                           107 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           43                           107 
[1] "AMP PEAK  5(2Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           44                           106 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           44                           106 
[1] "AMP PEAK  6(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          102                            48 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          102                            48 
[1] "AMP PEAK  7(4Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                           26                           124 
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                           26                           124 
[1] "AMP PEAK  8(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            79                             71 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            79                             71 
[1] "AMP PEAK  9(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           60                            90 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           60                            90 
[1] "AMP PEAK 10(6Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           35                           115 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           35                           115 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          102                            48 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          102                            48 
[1] "AMP PEAK 12(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           93                            57 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           93                            57 
[1] "AMP PEAK 13(8P23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           45                           105 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           45                           105 
[1] "AMP PEAK 14(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            72                             78 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            72                             78 
[1] "AMP PEAK 15(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           120                             30 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           120                             30 
[1] "AMP PEAK 16(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           31                           119 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           31                           119 
[1] "AMP PEAK 17(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           50                           100 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           50                           100 
[1] "AMP PEAK 18(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          44                          106 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          44                          106 
[1] "AMP PEAK 19(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          40                          110 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          40                          110 
[1] "AMP PEAK 20(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            81                             69 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            81                             69 
[1] "AMP PEAK 21(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            63                             87 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            63                             87 
[1] "AMP PEAK 22(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          38                          112 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          38                          112 
[1] "AMP PEAK 23(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            56                             94 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            56                             94 
[1] "AMP PEAK 24(14Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            46                            104 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            46                            104 
[1] "AMP PEAK 25(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            49                            101 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            49                            101 
[1] "AMP PEAK 26(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          60                           90 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          60                           90 
[1] "AMP PEAK 27(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             55                              95 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             55                              95 
[1] "AMP PEAK 28(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            48                            102 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            48                            102 
[1] "AMP PEAK 29(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                            26                            124 
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                            26                            124 
[1] "AMP PEAK 30(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          43                          107 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          43                          107 
[1] "AMP PEAK 31(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                         53                          97 
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                         53                          97 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            60                             90 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            60                             90 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           52                            98 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           52                            98 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         16                         134 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         16                         134 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           43                           107 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           43                           107 
[1] "DEL PEAK  5(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           25                           125 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           25                           125 
[1] "DEL PEAK  6(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                           85                            65 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                           85                            65 
[1] "DEL PEAK  7(3P14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           98                            52 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           98                            52 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           96                            54 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           96                            54 
[1] "DEL PEAK  9(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           26                           124 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           26                           124 
[1] "DEL PEAK 10(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            13                            137 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            13                            137 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           87                            63 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           87                            63 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           87                            63 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           87                            63 
[1] "DEL PEAK 13(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           84                            66 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           84                            66 
[1] "DEL PEAK 14(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                           92                            58 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                           92                            58 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           62                            88 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           62                            88 
[1] "DEL PEAK 16(6Q16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           41                           109 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           41                           109 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         42                         108 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         42                         108 
[1] "DEL PEAK 18(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           48                           102 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           48                           102 
[1] "DEL PEAK 19(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           58                            92 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           58                            92 
[1] "DEL PEAK 20(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           72                            78 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           72                            78 
[1] "DEL PEAK 21(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         60                          90 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         60                          90 
[1] "DEL PEAK 22(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                         86                          64 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                         86                          64 
[1] "DEL PEAK 23(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          112                            38 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          112                            38 
[1] "DEL PEAK 24(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            41                            109 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            41                            109 
[1] "DEL PEAK 25(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             37                             113 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             37                             113 
[1] "DEL PEAK 26(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            36                            114 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            36                            114 
[1] "DEL PEAK 27(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             54                              96 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             54                              96 
[1] "DEL PEAK 28(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            61                             89 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            61                             89 
[1] "DEL PEAK 29(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          63                           87 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          63                           87 
[1] "DEL PEAK 30(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            42                            108 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            42                            108 
[1] "DEL PEAK 31(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             59                              91 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             59                              91 
[1] "DEL PEAK 32(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            60                             90 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            60                             90 
[1] "DEL PEAK 33(13Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             56                              94 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             56                              94 
[1] "DEL PEAK 34(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            44                            106 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            44                            106 
[1] "DEL PEAK 35(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            50                            100 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            50                            100 
[1] "DEL PEAK 36(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            52                             98 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            52                             98 
[1] "DEL PEAK 37(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            71                             79 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            71                             79 
[1] "DEL PEAK 38(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          69                           81 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          69                           81 
[1] "DEL PEAK 39(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                            35                            115 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                            35                            115 
[1] "DEL PEAK 40(18P11.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             51                              99 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             51                              99 
[1] "DEL PEAK 41(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                            90                             60 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                            90                             60 
[1] "DEL PEAK 42(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            96                             54 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            96                             54 
[1] "DEL PEAK 43(18Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                            89                             61 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                            89                             61 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            75                             75 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            75                             75 
[1] "DEL PEAK 45(19Q11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                          40                          110 
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                          40                          110 
[1] "DEL PEAK 46(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            30                            120 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            30                            120 
[1] "DEL PEAK 47(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            87                             63 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            87                             63 
[1] "DEL PEAK 48(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                            87                             63 
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                            87                             63 
[1] "DEL PEAK 49(21Q22.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                             87                              63 
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                             87                              63 
[1] "DEL PEAK 50(22Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                            68                             82 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                            68                             82 
[1] "DEL PEAK 51(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           55                            95 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           55                            95 
[1] "DEL PEAK 52(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           59                            91 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           59                            91 
[1] "DEL PEAK 53(XQ11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                           35                           115 
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                           35                           115 
[1] "DEL PEAK 54(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                            33                            117 
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                            33                            117 
[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 150 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
          NA           NA           NA           NA           NA           NA 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
          NA           NA           NA           NA           NA         1012 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
         611           NA          632           80          612            1 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
           8           30           16          518           NA          712 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
          11            4          452           14           13           NA 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        3714           NA         1837         2069           NA           NA 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        1301          773          471          705          769          550 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
         535          189           96          105           NA           NA 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
         272          107          112          102          593          267 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
         195          124           NA          101          218           NA 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
          NA          935           NA          882           NA           NA 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
         211          265           79           NA           11          225 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
         120           92         1688           NA         1094           NA 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
          NA          501          412          402           NA          165 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
          NA          265          408          825           NA           NA 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
          NA          315            2          318            5            2 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
          10           NA            3            4            2            3 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
           2            3            2           NA            4            2 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
           3            3            3            2            2            3 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
           2            6           36           NA           NA           NA 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
          NA           NA          536           NA          115           NA 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
          NA           NA          447           NA          900           NA 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        1641           NA           NA          267          426           NA 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
          NA          146          258          248          135           NA 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
          NA         1117          366           NA           NA          551 
Variable 1:'AGE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=78,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=12,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=2,	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=38,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=11,	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 150 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=46, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
 1 25 33 74  4 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   26    33    74     4 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 25 33 74  4 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   26    33    74     4 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
64 54 11  6 
[1] "table(vv)"
vv
N0 N1 N2 N3 
64 54 11  6 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
64 54 11  6 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
64 54 11  6 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=38, binary=FALSE, numeric=TRUE
RACE, nv=3, 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   20  9
  AMP PEAK  1(1P34.2) WILD-TYPE 68 45
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           29                           113 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            9                            45 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-2H-A9GN TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FH 
        8.94        20.78        17.03         0.46       122.10        42.77 
TCGA-JY-A93E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A88Y 
       18.08         4.08        18.35         1.38         7.13         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NS 
        3.95         3.02        55.50         2.66        13.22        13.41 
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 TCGA-V5-A7RC TCGA-ZR-A9CJ 
       29.59         6.35        53.95         3.42        18.12 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
       13.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.43        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        15.48        23.18        25.28        17.59         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-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
        3.68         3.35        19.50         8.78         6.41         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         3.16        30.74         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NG 
        6.94         8.71         2.60        25.12         7.40        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36         0.07         0.16         0.07         0.33         0.10 
TCGA-LN-A49U TCGA-LN-A49V 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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.10         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        1.18        17.62         5.16         3.78         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       14.70         7.04         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
        5.29         4.80         8.48         8.15         4.44        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.12        36.72        12.03         9.17        15.91 

  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 
                         8.02                          7.43 
[1] "0.1 - 122.1 (8.0)" "0.0 - 83.2 (7.4)" 
[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       6        3        6        1        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P34.2) MUTATED           6         4          3          1
  AMP PEAK  1(1P34.2) WILD-TYPE        20        19          8          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  1(1P34.2) MUTATED            1        0         1
  AMP PEAK  1(1P34.2) WILD-TYPE          5        3         1
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             3
  STAGE IB                             0                             6
  STAGE II                             0                             1
  STAGE IIA                            4                            31
  STAGE IIB                            6                            20
  STAGE III                            4                            19
  STAGE IIIA                           3                             8
  STAGE IIIB                           1                             7
  STAGE IIIC                           1                             5
  STAGE IV                             0                             3
  STAGE IVA                            1                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  1(1P34.2) MUTATED       7  6 11  1
  AMP PEAK  1(1P34.2) WILD-TYPE    19 27 63  3
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T0+T1                           7                            19
  T2                              6                            27
  T3                             11                            63
  T4                              1                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  1(1P34.2) MUTATED   11 11  2  1
  AMP PEAK  1(1P34.2) WILD-TYPE 53 43  9  5
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                          11                            53
  N1                          11                            43
  N2                           2                             9
  N3                           1                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  1(1P34.2) MUTATED   19  0   1  3
  AMP PEAK  1(1P34.2) WILD-TYPE 92  2   2 14
D1V6, multiclass
     clus
vv    AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  M0                           19                            92
  M1                            0                             2
  M1A                           1                             2
  MX                            3                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED     3  27
  AMP PEAK  1(1P34.2) WILD-TYPE  18 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      3   27
  AMP PEAK  1(1P34.2) WILD-TYPE   18  102
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                           3                            18
  MALE                            27                           102
[1] 2 2
[1] FALSE
D1V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P34.2) MUTATED       7                         1    20
  AMP PEAK  1(1P34.2) WILD-TYPE    31                         1    73
D1V9, multiclass
                           clus
vv                          AMP PEAK  1(1P34.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              20
                           clus
vv                          AMP PEAK  1(1P34.2) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1Q23.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q23.3) MUTATED   43 27
  AMP PEAK  2(1Q23.3) WILD-TYPE 45 27
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           70                            72 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           27                            27 
$`AMP PEAK  2(1Q23.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        58.55        13.94         8.94        16.24         4.21 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         0.85        20.12         0.03         0.26         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03         0.79        23.41         0.36         0.46         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93E 
      122.10        44.75        60.39         3.68        25.28        18.08 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        19.50         8.78         6.41         4.08        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y 
        7.17         1.38         4.90         7.43         2.60         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.95         3.02        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49K 
       16.47        13.22         5.42        13.41        52.57         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 
       10.45         0.16         0.13         0.07         0.10         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6DN 
        0.07         0.07         0.10         0.07         0.20         8.02 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW 
       14.70        29.59         6.35        53.95         8.78        14.01 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EW TCGA-ZR-A9CJ 
        3.42         4.80         8.12        18.12 

$`AMP PEAK  2(1Q23.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78        14.30         7.63         5.92        32.45        33.27 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FD 
       20.78         2.63         0.99         0.13        14.86        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F 
       41.52        42.77        25.41        15.48        23.18        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        6.21         3.16         3.45         4.31         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        3.68         3.35         3.32         3.16        30.74        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NG TCGA-L5-A8NI 
        7.13         6.94         8.71        25.12        35.97        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU 
       13.55         7.76        21.37         8.71        27.12        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W 
       46.09        10.36         0.07         0.33         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.10         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        1.18        17.62         5.16         3.78         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        7.04         9.30         7.00         5.29         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        4.44        18.31        36.72        12.03         9.17        15.91 

  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                        6.790                         7.955 
[1] "0.0 - 122.1 (6.8)" "0.1 - 83.2 (8.0)" 
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q23.3) MUTATED         6        2        3        0        14
  AMP PEAK  2(1Q23.3) WILD-TYPE       2        2        3        1        21
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q23.3) MUTATED          12        10          6          4
  AMP PEAK  2(1Q23.3) WILD-TYPE        14        13          5          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  2(1Q23.3) MUTATED            3        2         2
  AMP PEAK  2(1Q23.3) WILD-TYPE          3        1         0
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  STAGE I                              6                             2
  STAGE IA                             2                             2
  STAGE IB                             3                             3
  STAGE II                             0                             1
  STAGE IIA                           14                            21
  STAGE IIB                           12                            14
  STAGE III                           10                            13
  STAGE IIIA                           6                             5
  STAGE IIIB                           4                             4
  STAGE IIIC                           3                             3
  STAGE IV                             2                             1
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  2(1Q23.3) MUTATED      17 14 34  1
  AMP PEAK  2(1Q23.3) WILD-TYPE     9 19 40  3
D2V4, multiclass
       clus
vv      AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  T0+T1                          17                             9
  T2                             14                            19
  T3                             34                            40
  T4                              1                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  2(1Q23.3) MUTATED   30 27  5  3
  AMP PEAK  2(1Q23.3) WILD-TYPE 34 27  6  3
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  N0                          30                            34
  N1                          27                            27
  N2                           5                             6
  N3                           3                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  2(1Q23.3) MUTATED   52  1   3  8
  AMP PEAK  2(1Q23.3) WILD-TYPE 59  1   0  9
D2V6, multiclass
     clus
vv    AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  M0                           52                            59
  M1                            1                             1
  M1A                           3                             0
  MX                            8                             9
[1] 4 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(1Q23.3) MUTATED    6 66
  AMP PEAK  2(1Q23.3) WILD-TYPE 15 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q23.3) MUTATED      6   66
  AMP PEAK  2(1Q23.3) WILD-TYPE   15   63
        clus
vv       AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  FEMALE                           6                            15
  MALE                            66                            63
[1] 2 2
[1] FALSE
D2V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q23.3) MUTATED      20                         1    45
  AMP PEAK  2(1Q23.3) WILD-TYPE    18                         1    48
D2V9, multiclass
                           clus
vv                          AMP PEAK  2(1Q23.3) MUTATED
  ASIAN                                              20
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              45
                           clus
vv                          AMP PEAK  2(1Q23.3) WILD-TYPE
  ASIAN                                                18
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(1Q42.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(1Q42.3) MUTATED   45 27
  AMP PEAK  3(1Q42.3) WILD-TYPE 43 27
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           72                            70 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           27                            27 
$`AMP PEAK  3(1Q42.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3QL 
       25.78        31.27        13.94         8.94        16.24        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63        20.12         0.03         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.79        23.41         0.36         0.46         0.43       122.10 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H 
       60.39         3.68        42.77        25.28        18.08         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        3.68        19.50         4.08        18.35         7.17         1.38 
TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        4.90         7.43         2.60         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL 
        3.02        55.50         2.66        12.92        13.48        13.22 
TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        5.42        52.57        46.09        10.36         0.07        10.45 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.13         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6KZ 
        0.07         0.07         0.10         0.07         0.20         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RC 
       14.70        29.59         6.35        53.95        14.01         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-ZR-A9CJ 
        4.80         8.15         8.12        36.72        15.91        18.12 

$`AMP PEAK  3(1Q42.3) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR 
       14.30        58.55         7.63         5.92         4.21        32.45 
TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A6QS TCGA-IG-A7DP 
       33.27        20.78         0.26         0.99         0.13        14.86 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        25.41        15.48        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M 
       17.59         6.21         3.16         3.45         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR 
        3.52         3.35         8.78         6.41         3.32         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-A8NG TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       35.97        16.47        13.55         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       13.41        27.12        83.24         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10         0.10         0.07         0.10         0.10         0.10 
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-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV 
        7.04         9.30         7.00         8.78         5.29         8.48 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7D 
        4.44        18.31        12.03         9.17 

  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                         6.76                          7.89 
[1] "0.0 - 122.1 (6.8)" "0.1 - 83.2 (7.9)" 
[1] "hr=" "1"  
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(1Q42.3) MUTATED         4        2        4        0        15
  AMP PEAK  3(1Q42.3) WILD-TYPE       4        2        2        1        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(1Q42.3) MUTATED          12        12          7          3
  AMP PEAK  3(1Q42.3) WILD-TYPE        14        11          4          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  3(1Q42.3) MUTATED            3        2         2
  AMP PEAK  3(1Q42.3) WILD-TYPE          3        1         0
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             2                             2
  STAGE IB                             4                             2
  STAGE II                             0                             1
  STAGE IIA                           15                            20
  STAGE IIB                           12                            14
  STAGE III                           12                            11
  STAGE IIIA                           7                             4
  STAGE IIIB                           3                             5
  STAGE IIIC                           3                             3
  STAGE IV                             2                             1
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  3(1Q42.3) MUTATED      16 16 34  2
  AMP PEAK  3(1Q42.3) WILD-TYPE    10 17 40  2
D3V4, multiclass
       clus
vv      AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T0+T1                          16                            10
  T2                             16                            17
  T3                             34                            40
  T4                              2                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  3(1Q42.3) MUTATED   29 31  4  3
  AMP PEAK  3(1Q42.3) WILD-TYPE 35 23  7  3
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  N0                          29                            35
  N1                          31                            23
  N2                           4                             7
  N3                           3                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  3(1Q42.3) MUTATED   54  1   3  7
  AMP PEAK  3(1Q42.3) WILD-TYPE 57  1   0 10
D3V6, multiclass
     clus
vv    AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  M0                           54                            57
  M1                            1                             1
  M1A                           3                             0
  MX                            7                            10
[1] 4 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(1Q42.3) MUTATED    5 70
  AMP PEAK  3(1Q42.3) WILD-TYPE 16 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      5   70
  AMP PEAK  3(1Q42.3) WILD-TYPE   16   59
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                           5                            16
  MALE                            70                            59
[1] 2 2
[1] FALSE
D3V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q42.3) MUTATED      21                         1    48
  AMP PEAK  3(1Q42.3) WILD-TYPE    17                         1    45
D3V9, multiclass
                           clus
vv                          AMP PEAK  3(1Q42.3) MUTATED
  ASIAN                                              21
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              48
                           clus
vv                          AMP PEAK  3(1Q42.3) WILD-TYPE
  ASIAN                                                17
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(2Q14.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(2Q14.2) MUTATED   27 13
  AMP PEAK  4(2Q14.2) WILD-TYPE 61 41
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           40                           102 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           13                            41 
$`AMP PEAK  4(2Q14.2) MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-IG-A97H 
       13.94         8.94        20.09         2.63        23.41         0.43 
TCGA-JY-A6FA TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH 
       44.75        25.28        18.08         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-L5-A8NE TCGA-L5-A8NR TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W 
       55.50         8.71        52.57         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.13         0.10         0.10         0.20         1.18 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        3.78         7.59         5.06        14.70         7.04         6.35 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       14.01         3.42         4.80         8.48 

$`AMP PEAK  4(2Q14.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         4.21        32.45        33.27         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12         0.03         0.26         0.99         0.53        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        14.86         0.46       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       15.48        23.18        17.59         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        0.30         3.52         3.68         3.35         8.78         6.41 
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-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         6.94         8.71        25.12         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS 
       13.55        13.22         7.76         5.42        21.37        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       27.12        83.24        46.09        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 TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
        7.00         8.78         5.29         8.15         4.44        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.12        36.72        12.03         9.17        15.91        18.12 

  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                         55.5                         122.1 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                        4.930                         8.135 
[1] "0.1 - 55.5 (4.9)"  "0.0 - 122.1 (8.1)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(2Q14.2) MUTATED         1        1        2        1         8
  AMP PEAK  4(2Q14.2) WILD-TYPE       7        3        4        0        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(2Q14.2) MUTATED           9         7          3          1
  AMP PEAK  4(2Q14.2) WILD-TYPE        17        16          8          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  4(2Q14.2) MUTATED            2        0         0
  AMP PEAK  4(2Q14.2) WILD-TYPE          4        3         2
D4V3, multiclass
            clus
vv           AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             1                             3
  STAGE IB                             2                             4
  STAGE II                             1                             0
  STAGE IIA                            8                            27
  STAGE IIB                            9                            17
  STAGE III                            7                            16
  STAGE IIIA                           3                             8
  STAGE IIIB                           1                             7
  STAGE IIIC                           2                             4
  STAGE IV                             0                             3
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  4(2Q14.2) MUTATED       5 10 22  0
  AMP PEAK  4(2Q14.2) WILD-TYPE    21 23 52  4
D4V4, multiclass
       clus
vv      AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  T0+T1                           5                            21
  T2                             10                            23
  T3                             22                            52
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  4(2Q14.2) MUTATED   17 14  3  2
  AMP PEAK  4(2Q14.2) WILD-TYPE 47 40  8  4
D4V5, multiclass
    clus
vv   AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  N0                          17                            47
  N1                          14                            40
  N2                           3                             8
  N3                           2                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  4(2Q14.2) MUTATED   29  0   0  7
  AMP PEAK  4(2Q14.2) WILD-TYPE 82  2   3 10
D4V6, multiclass
     clus
vv    AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  M0                           29                            82
  M1                            0                             2
  M1A                           0                             3
  MX                            7                            10
[1] 4 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(2Q14.2) MUTATED    5 38
  AMP PEAK  4(2Q14.2) WILD-TYPE 16 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q14.2) MUTATED      5   38
  AMP PEAK  4(2Q14.2) WILD-TYPE   16   91
        clus
vv       AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  FEMALE                           5                            16
  MALE                            38                            91
[1] 2 2
[1] FALSE
D4V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2Q14.2) MUTATED      14                         2    23
  AMP PEAK  4(2Q14.2) WILD-TYPE    24                         0    70
D4V9, multiclass
                           clus
vv                          AMP PEAK  4(2Q14.2) MUTATED
  ASIAN                                              14
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              23
                           clus
vv                          AMP PEAK  4(2Q14.2) WILD-TYPE
  ASIAN                                                24
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(2Q31.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(2Q31.1) MUTATED   26 15
  AMP PEAK  5(2Q31.1) WILD-TYPE 62 39
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           41                           101 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           15                            39 
$`AMP PEAK  5(2Q31.1) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A5S3 
       58.55        13.94         8.94         2.63         0.26        23.41 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OH TCGA-L5-A4OM 
        0.46         0.43        18.08         4.31        19.50         4.08 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NE 
        3.32         1.38         6.94         2.60         0.36        55.50 
TCGA-L5-A8NI TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       13.48        52.57         0.07         0.10         0.07         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.13         0.10         0.20         1.18         3.78         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BW 
        5.06        14.70        29.59         6.35        53.95        14.01 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW 
        3.42         4.80         8.48        18.31         8.12 

$`AMP PEAK  5(2Q31.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63         5.92        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         0.03         0.99         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.36         0.13        14.86       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.28        17.59         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
        0.30         8.94         3.52         3.68         3.35         8.78 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        6.41        18.35         7.17         3.16        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-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.95         3.02         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        27.12        83.24        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X 
        0.16         0.07         0.33         0.13         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6L6 
        0.10         0.07        17.62         5.16         8.02         7.04 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX 
        9.30         7.00         8.78         5.29         8.15         4.44 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        12.03         9.17        15.91        18.12 

  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                        58.55                        122.10 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                         4.80                          8.15 
[1] "0.1 - 58.5 (4.8)"  "0.0 - 122.1 (8.2)"
[1] "hr=" "1.2"
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(2Q31.1) MUTATED         2        1        3        1         9
  AMP PEAK  5(2Q31.1) WILD-TYPE       6        3        3        0        26
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(2Q31.1) MUTATED           6         5          3          4
  AMP PEAK  5(2Q31.1) WILD-TYPE        20        18          8          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  5(2Q31.1) MUTATED            1        1         0
  AMP PEAK  5(2Q31.1) WILD-TYPE          5        2         2
D5V3, multiclass
            clus
vv           AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             3
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                            9                            26
  STAGE IIB                            6                            20
  STAGE III                            5                            18
  STAGE IIIA                           3                             8
  STAGE IIIB                           4                             4
  STAGE IIIC                           1                             5
  STAGE IV                             1                             2
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  5(2Q31.1) MUTATED       7  7 23  0
  AMP PEAK  5(2Q31.1) WILD-TYPE    19 26 51  4
D5V4, multiclass
       clus
vv      AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  T0+T1                           7                            19
  T2                              7                            26
  T3                             23                            51
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  5(2Q31.1) MUTATED   19 11  5  1
  AMP PEAK  5(2Q31.1) WILD-TYPE 45 43  6  5
D5V5, multiclass
    clus
vv   AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  N0                          19                            45
  N1                          11                            43
  N2                           5                             6
  N3                           1                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  5(2Q31.1) MUTATED   28  1   0  7
  AMP PEAK  5(2Q31.1) WILD-TYPE 83  1   3 10
D5V6, multiclass
     clus
vv    AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  M0                           28                            83
  M1                            1                             1
  M1A                           0                             3
  MX                            7                            10
[1] 4 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(2Q31.1) MUTATED    3 41
  AMP PEAK  5(2Q31.1) WILD-TYPE 18 88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.1) MUTATED      3   41
  AMP PEAK  5(2Q31.1) WILD-TYPE   18   88
        clus
vv       AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  FEMALE                           3                            18
  MALE                            41                            88
[1] 2 2
[1] FALSE
D5V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(2Q31.1) MUTATED      14                         2    25
  AMP PEAK  5(2Q31.1) WILD-TYPE    24                         0    68
D5V9, multiclass
                           clus
vv                          AMP PEAK  5(2Q31.1) MUTATED
  ASIAN                                              14
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              25
                           clus
vv                          AMP PEAK  5(2Q31.1) WILD-TYPE
  ASIAN                                                24
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(3Q26.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(3Q26.2) MUTATED   58 36
  AMP PEAK  6(3Q26.2) WILD-TYPE 30 18
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                           94                            48 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                           36                            18 
$`AMP PEAK  6(3Q26.2) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO 
       31.27        14.30        58.55         7.63         5.92        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         0.03         0.26         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41         0.36         0.13         0.46         0.43 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E 
       44.75        60.39         3.68        42.77        23.18        18.08 
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-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        6.94         2.60         7.40        55.50         2.66        35.97 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       16.47        13.22         5.42         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
        0.33         0.10         0.13         0.10         0.07         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-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BW 
        8.02         7.59         5.06         6.35        53.95        14.01 
TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 
        3.42         8.15         4.44        18.31         8.12        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       12.03         9.17        15.91        18.12 

$`AMP PEAK  6(3Q26.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6F8 
       25.78        13.94         8.94         0.99        14.86       122.10 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
       68.02        41.52        25.41        15.48        25.28        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        6.21         3.16         8.94         3.68         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88T 
        8.78         6.41        30.74         4.90         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         0.36         3.95         3.02        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49U 
       13.55         7.76        21.37        83.24        46.09         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 TCGA-V5-AASV 
        9.30         7.00         8.78         5.29         4.80         8.48 

  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                        60.39                        122.10 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                         5.67                          8.94 
[1] "0.0 - 60.4 (5.7)"  "0.1 - 122.1 (8.9)"
[1] "hr=" "1.5"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(3Q26.2) MUTATED         3        3        3        1        26
  AMP PEAK  6(3Q26.2) WILD-TYPE       5        1        3        0         9
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(3Q26.2) MUTATED          16        19          9          7
  AMP PEAK  6(3Q26.2) WILD-TYPE        10         4          2          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  6(3Q26.2) MUTATED            4        1         2
  AMP PEAK  6(3Q26.2) WILD-TYPE          2        2         0
D6V3, multiclass
            clus
vv           AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             3                             1
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                           26                             9
  STAGE IIB                           16                            10
  STAGE III                           19                             4
  STAGE IIIA                           9                             2
  STAGE IIIB                           7                             1
  STAGE IIIC                           4                             2
  STAGE IV                             1                             2
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  6(3Q26.2) MUTATED      12 24 55  3
  AMP PEAK  6(3Q26.2) WILD-TYPE    14  9 19  1
D6V4, multiclass
       clus
vv      AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  T0+T1                          12                            14
  T2                             24                             9
  T3                             55                            19
  T4                              3                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  6(3Q26.2) MUTATED   43 37  9  4
  AMP PEAK  6(3Q26.2) WILD-TYPE 21 17  2  2
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  N0                          43                            21
  N1                          37                            17
  N2                           9                             2
  N3                           4                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  6(3Q26.2) MUTATED   79  1   2  9
  AMP PEAK  6(3Q26.2) WILD-TYPE 32  1   1  8
D6V6, multiclass
     clus
vv    AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  M0                           79                            32
  M1                            1                             1
  M1A                           2                             1
  MX                            9                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                             0  1
  AMP PEAK  6(3Q26.2) MUTATED   10 92
  AMP PEAK  6(3Q26.2) WILD-TYPE 11 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED     10   92
  AMP PEAK  6(3Q26.2) WILD-TYPE   11   37
        clus
vv       AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  FEMALE                          10                            11
  MALE                            92                            37
[1] 2 2
[1] FALSE
D6V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.2) MUTATED      35                         1    55
  AMP PEAK  6(3Q26.2) WILD-TYPE     3                         1    38
D6V9, multiclass
                           clus
vv                          AMP PEAK  6(3Q26.2) MUTATED
  ASIAN                                              35
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              55
                           clus
vv                          AMP PEAK  6(3Q26.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(4Q21.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(4Q21.1) MUTATED   18  6
  AMP PEAK  7(4Q21.1) WILD-TYPE 70 48
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                           24                           118 
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                            6                            48 
$`AMP PEAK  7(4Q21.1) MUTATED`
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-JY-A6FA 
       20.78         2.63         0.53        23.41       122.10        44.75 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OS TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NN 
       18.35         3.32        30.74        55.50        13.48         5.42 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49R TCGA-LN-A49X TCGA-LN-A4A8 
        8.71        27.12        83.24         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-S8-A6BV TCGA-V5-A7RC TCGA-VR-A8EW TCGA-VR-AA4G 
        0.07         3.78         8.78         3.42         8.12        12.03 

$`AMP PEAK  7(4Q21.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09         0.85        20.12         0.03         0.26         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        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        0.43        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        15.48        23.18        25.28        18.08        17.59 
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-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        4.08         7.17         1.38         3.16         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-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.95         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       13.41        52.57        46.09        10.36         0.07        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-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.10         0.10         0.07         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         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 TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
        5.29         4.80         8.48         8.15         4.44        18.31 
TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72         9.17        15.91        18.12 

  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                       122.10                         68.02 
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                        8.745                         7.285 
[1] "0.1 - 122.1 (8.7)" "0.0 - 68.0 (7.3)" 
[1] "hr=" "2.6"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(4Q21.1) MUTATED         1        0        0        0         5
  AMP PEAK  7(4Q21.1) WILD-TYPE       7        4        6        1        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(4Q21.1) MUTATED           6         5          5          2
  AMP PEAK  7(4Q21.1) WILD-TYPE        20        18          6          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  7(4Q21.1) MUTATED            1        0         0
  AMP PEAK  7(4Q21.1) WILD-TYPE          5        3         2
D7V3, multiclass
            clus
vv           AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             0                             4
  STAGE IB                             0                             6
  STAGE II                             0                             1
  STAGE IIA                            5                            30
  STAGE IIB                            6                            20
  STAGE III                            5                            18
  STAGE IIIA                           5                             6
  STAGE IIIB                           2                             6
  STAGE IIIC                           1                             5
  STAGE IV                             0                             3
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  7(4Q21.1) MUTATED       2  8 14  1
  AMP PEAK  7(4Q21.1) WILD-TYPE    24 25 60  3
D7V4, multiclass
       clus
vv      AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  T0+T1                           2                            24
  T2                              8                            25
  T3                             14                            60
  T4                              1                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  7(4Q21.1) MUTATED    9 12  3  1
  AMP PEAK  7(4Q21.1) WILD-TYPE 55 42  8  5
D7V5, multiclass
    clus
vv   AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  N0                           9                            55
  N1                          12                            42
  N2                           3                             8
  N3                           1                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  7(4Q21.1) MUTATED   23  0   0  1
  AMP PEAK  7(4Q21.1) WILD-TYPE 88  2   3 16
D7V6, multiclass
     clus
vv    AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  M0                           23                            88
  M1                            0                             2
  M1A                           0                             3
  MX                            1                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(4Q21.1) MUTATED     4  22
  AMP PEAK  7(4Q21.1) WILD-TYPE  17 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q21.1) MUTATED      4   22
  AMP PEAK  7(4Q21.1) WILD-TYPE   17  107
        clus
vv       AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  FEMALE                           4                            17
  MALE                            22                           107
[1] 2 2
[1] FALSE
D7V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4Q21.1) MUTATED       9                         1    15
  AMP PEAK  7(4Q21.1) WILD-TYPE    29                         1    78
D7V9, multiclass
                           clus
vv                          AMP PEAK  7(4Q21.1) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              15
                           clus
vv                          AMP PEAK  7(4Q21.1) WILD-TYPE
  ASIAN                                                29
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(5P15.33) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(5P15.33) MUTATED   52 21
  AMP PEAK  8(5P15.33) WILD-TYPE 36 33
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            73                             69 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            21                             33 
$`AMP PEAK  8(5P15.33) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC 
       14.30         5.92        32.45        33.27         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H 
        0.03         0.53         0.79        23.41         0.46         0.43 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
       44.75        68.02         3.68        42.77        25.28        18.08 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI 
        3.16         0.30         4.31         8.94        19.50         8.78 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        4.08         7.17         3.16         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG 
        6.94         2.60         0.36         3.95        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       12.92        16.47        13.55        13.41        27.12        52.57 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.36         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.10         0.07         0.10         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-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BW 
        5.06        14.70        29.59        53.95         7.00        14.01 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I 
        3.42         4.80        18.31        36.72        12.03        15.91 
TCGA-ZR-A9CJ 
       18.12 

$`AMP PEAK  8(5P15.33) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS 
       16.24         4.21        20.09         0.85        20.78         0.26 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 
        0.99        17.03         0.36         0.13        14.86       122.10 
TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F 
       60.39        41.52        25.41        15.48        23.18        17.59 
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-A8NF TCGA-L5-A8NI TCGA-L5-A8NL 
       25.12         7.40         3.02         2.66        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW 
        7.76         5.42        21.37         8.71        83.24        46.09 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 
       10.45         0.16         0.07         0.10         0.13         0.07 
TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
        0.07        17.62         3.78         8.02         7.59         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        6.35         9.30         8.78         5.29         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA7D 
        4.44         8.12         9.17 

  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                         68.02                         122.10 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                          5.92                           8.12 
[1] "0.0 - 68.0 (5.9)"  "0.1 - 122.1 (8.1)"
[1] "hr=" "1.4"
D8V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(5P15.33) MUTATED         1        3        4        1        22
  AMP PEAK  8(5P15.33) WILD-TYPE       7        1        2        0        13
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(5P15.33) MUTATED          11        13          6          2
  AMP PEAK  8(5P15.33) WILD-TYPE        15        10          5          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  8(5P15.33) MUTATED            4        3         0
  AMP PEAK  8(5P15.33) WILD-TYPE          2        0         2
D8V3, multiclass
            clus
vv           AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              3                              1
  STAGE IB                              4                              2
  STAGE II                              1                              0
  STAGE IIA                            22                             13
  STAGE IIB                            11                             15
  STAGE III                            13                             10
  STAGE IIIA                            6                              5
  STAGE IIIB                            2                              6
  STAGE IIIC                            4                              2
  STAGE IV                              3                              0
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK  8(5P15.33) MUTATED       9 18 45  1
  AMP PEAK  8(5P15.33) WILD-TYPE    17 15 29  3
D8V4, multiclass
       clus
vv      AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  T0+T1                            9                             17
  T2                              18                             15
  T3                              45                             29
  T4                               1                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK  8(5P15.33) MUTATED   37 27  4  4
  AMP PEAK  8(5P15.33) WILD-TYPE 27 27  7  2
D8V5, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  N0                           37                             27
  N1                           27                             27
  N2                            4                              7
  N3                            4                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK  8(5P15.33) MUTATED   58  2   1 11
  AMP PEAK  8(5P15.33) WILD-TYPE 53  0   2  6
D8V6, multiclass
     clus
vv    AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  M0                            58                             53
  M1                             2                              0
  M1A                            1                              2
  MX                            11                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   11 68
  AMP PEAK  8(5P15.33) WILD-TYPE 10 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     11   68
  AMP PEAK  8(5P15.33) WILD-TYPE   10   61
        clus
vv       AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  FEMALE                           11                             10
  MALE                             68                             61
[1] 2 2
[1] FALSE
D8V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(5P15.33) MUTATED      27                         1    46
  AMP PEAK  8(5P15.33) WILD-TYPE    11                         1    47
D8V9, multiclass
                           clus
vv                          AMP PEAK  8(5P15.33) MUTATED
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               46
                           clus
vv                          AMP PEAK  8(5P15.33) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(6P21.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  9(6P21.1) MUTATED   32 25
  AMP PEAK  9(6P21.1) WILD-TYPE 56 29
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           57                            85 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           25                            29 
$`AMP PEAK  9(6P21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
       16.24         4.21         0.26         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A939 TCGA-L5-A43E TCGA-L5-A4OM TCGA-L5-A4ON 
       60.39        68.02        15.48         3.45         4.08        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
        7.17         1.38        30.74         7.13         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NV 
       12.92        13.48         5.42        21.37        27.12        52.57 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V 
       10.36         0.07        10.45         0.33         0.13         0.10 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-R6-A6DN 
        0.10         0.13         0.07         0.10         0.20         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BV 
        7.59        14.70         7.04        29.59        53.95         8.78 
TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-AA7I 
        3.42         4.44        15.91 

$`AMP PEAK  9(6P21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       31.27         5.92        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         0.03         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A97H TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
        0.43         3.68        41.52        42.77        25.41        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       25.28        18.08        17.59         6.21         3.16         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-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        8.78         6.41         3.32         3.16         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.43         8.71        25.12         7.40        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
       13.22         7.76         8.71        13.41        83.24        46.09 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y 
        0.16         0.07         0.10         0.07         0.07         0.07 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6XQ 
        1.18        17.62         5.16         3.78         5.06         6.35 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        9.30         7.00        14.01         5.29         4.80         8.48 
TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        8.15        18.31         8.12        36.72        12.03         9.17 
TCGA-ZR-A9CJ 
       18.12 

  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                         7.63                          7.40 
[1] "0.1 - 122.1 (7.6)" "0.0 - 83.2 (7.4)" 
[1] "hr=" "1"  
D9V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6P21.1) MUTATED         5        2        1        0        14
  AMP PEAK  9(6P21.1) WILD-TYPE       3        2        5        1        21
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6P21.1) MUTATED           9        11          2          2
  AMP PEAK  9(6P21.1) WILD-TYPE        17        12          9          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  9(6P21.1) MUTATED            1        1         2
  AMP PEAK  9(6P21.1) WILD-TYPE          5        2         0
D9V3, multiclass
            clus
vv           AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             2
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           14                            21
  STAGE IIB                            9                            17
  STAGE III                           11                            12
  STAGE IIIA                           2                             9
  STAGE IIIB                           2                             6
  STAGE IIIC                           1                             5
  STAGE IV                             1                             2
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  9(6P21.1) MUTATED      13 12 26  1
  AMP PEAK  9(6P21.1) WILD-TYPE    13 21 48  3
D9V4, multiclass
       clus
vv      AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  T0+T1                          13                            13
  T2                             12                            21
  T3                             26                            48
  T4                              1                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  9(6P21.1) MUTATED   27 21  3  1
  AMP PEAK  9(6P21.1) WILD-TYPE 37 33  8  5
D9V5, multiclass
    clus
vv   AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  N0                          27                            37
  N1                          21                            33
  N2                           3                             8
  N3                           1                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  9(6P21.1) MUTATED   40  1   2  7
  AMP PEAK  9(6P21.1) WILD-TYPE 71  1   1 10
D9V6, multiclass
     clus
vv    AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  M0                           40                            71
  M1                            1                             1
  M1A                           2                             1
  MX                            7                            10
[1] 4 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(6P21.1) MUTATED    7 53
  AMP PEAK  9(6P21.1) WILD-TYPE 14 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      7   53
  AMP PEAK  9(6P21.1) WILD-TYPE   14   76
        clus
vv       AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  FEMALE                           7                            14
  MALE                            53                            76
[1] 2 2
[1] FALSE
D9V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6P21.1) MUTATED      15                         1    35
  AMP PEAK  9(6P21.1) WILD-TYPE    23                         1    58
D9V9, multiclass
                           clus
vv                          AMP PEAK  9(6P21.1) MUTATED
  ASIAN                                              15
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              35
                           clus
vv                          AMP PEAK  9(6P21.1) WILD-TYPE
  ASIAN                                                23
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(6Q23.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(6Q23.3) MUTATED   17 16
  AMP PEAK 10(6Q23.3) WILD-TYPE 71 38
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           33                           109 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           16                            38 
$`AMP PEAK 10(6Q23.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS TCGA-JY-A6F8 
       31.27        14.30        13.94        16.24         0.26       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A4OG TCGA-L5-A4OW 
       60.39        68.02        25.41         3.45         3.35         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.43         6.94         3.95         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L 
       12.92        13.48        21.37        27.12        10.36        10.45 
TCGA-LN-A49S TCGA-LN-A49V TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13         0.10        17.62         8.02        14.70         7.04 
TCGA-VR-A8EU TCGA-VR-AA7I TCGA-ZR-A9CJ 
       18.31        15.91        18.12 

$`AMP PEAK 10(6Q23.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78        58.55         7.63         5.92         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         0.03         0.99         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41         0.36         0.13        14.86         0.46         0.43 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75         3.68        41.52        42.77        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       25.28        18.08        17.59         6.21         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        4.31         8.94         3.52         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-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V 
        3.16        30.74         4.90        29.00         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NK 
       25.12         0.36         7.40        35.97        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.42         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09         0.07         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.10         0.07         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-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.07         0.20         1.18         5.16         3.78 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         5.06        29.59         6.35        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00         8.78        14.01         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.48         8.15         4.44         8.12        36.72        12.03 
TCGA-VR-AA7D 
        9.17 

  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                        13.48                          6.35 
[1] "0.1 - 122.1 (13.5)" "0.0 - 83.2 (6.3)"  
[1] "hr=" "1.1"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(6Q23.3) MUTATED         5        0        1        0         7
  AMP PEAK 10(6Q23.3) WILD-TYPE       3        4        5        1        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(6Q23.3) MUTATED           7         4          0          1
  AMP PEAK 10(6Q23.3) WILD-TYPE        19        19         11          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(6Q23.3) MUTATED            2        2         2
  AMP PEAK 10(6Q23.3) WILD-TYPE          4        1         0
D10V3, multiclass
            clus
vv           AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             0                             4
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                            7                            28
  STAGE IIB                            7                            19
  STAGE III                            4                            19
  STAGE IIIA                           0                            11
  STAGE IIIB                           1                             7
  STAGE IIIC                           2                             4
  STAGE IV                             2                             1
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 10(6Q23.3) MUTATED      10  6 15  1
  AMP PEAK 10(6Q23.3) WILD-TYPE    16 27 59  3
D10V4, multiclass
       clus
vv      AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  T0+T1                          10                            16
  T2                              6                            27
  T3                             15                            59
  T4                              1                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 10(6Q23.3) MUTATED   18 11  1  2
  AMP PEAK 10(6Q23.3) WILD-TYPE 46 43 10  4
D10V5, multiclass
    clus
vv   AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  N0                          18                            46
  N1                          11                            43
  N2                           1                            10
  N3                           2                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK 10(6Q23.3) MUTATED   25  2   2  3
  AMP PEAK 10(6Q23.3) WILD-TYPE 86  0   1 14
D10V6, multiclass
     clus
vv    AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  M0                           25                            86
  M1                            2                             0
  M1A                           2                             1
  MX                            3                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                             0  1
  AMP PEAK 10(6Q23.3) MUTATED    4 31
  AMP PEAK 10(6Q23.3) WILD-TYPE 17 98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6Q23.3) MUTATED      4   31
  AMP PEAK 10(6Q23.3) WILD-TYPE   17   98
        clus
vv       AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  FEMALE                           4                            17
  MALE                            31                            98
[1] 2 2
[1] FALSE
D10V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6Q23.3) MUTATED       6                         0    23
  AMP PEAK 10(6Q23.3) WILD-TYPE    32                         2    70
D10V9, multiclass
                           clus
vv                          AMP PEAK 10(6Q23.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              23
                           clus
vv                          AMP PEAK 10(6Q23.3) WILD-TYPE
  ASIAN                                                32
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(7P11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 11(7P11.2) MUTATED   64 35
  AMP PEAK 11(7P11.2) WILD-TYPE 24 19
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           99                            43 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           35                            19 
$`AMP PEAK 11(7P11.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
       32.45        20.09         0.85        20.12         0.03         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB 
       17.03         0.79        23.41         0.43        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       68.02        15.48        23.18        18.08         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-A8NE TCGA-L5-A8NF 
        2.60         0.36         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       35.97        12.92        16.47        13.55        13.22         5.42 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        52.57        46.09        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 TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW 
        5.29         3.42         8.48         8.15         4.44         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        15.91        18.12 

$`AMP PEAK 11(7P11.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3YA 
       31.27        14.30        58.55         4.21        33.27        20.78 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        2.63         0.26         0.99         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
        0.46       122.10         3.68        41.52        42.77        25.41 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OP 
       25.28        17.59         6.21         8.94         8.78         7.17 
TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ 
        7.43        25.12         7.40        13.48         7.76        21.37 
TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A4A5 
       83.24        10.45         0.16         0.07         0.13         0.10 
TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-V5-A7RE TCGA-VR-A8EU TCGA-VR-AA4G 
        0.07        17.62        29.59         4.80        18.31        12.03 
TCGA-VR-AA7D 
        9.17 

  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                        68.02                        122.10 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                         6.94                          9.17 
[1] "0.0 - 68.0 (6.9)"  "0.1 - 122.1 (9.2)"
[1] "hr=" "1.1"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7P11.2) MUTATED         6        2        4        1        18
  AMP PEAK 11(7P11.2) WILD-TYPE       2        2        2        0        17
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(7P11.2) MUTATED          19        18          7          5
  AMP PEAK 11(7P11.2) WILD-TYPE         7         5          4          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 11(7P11.2) MUTATED            3        2         2
  AMP PEAK 11(7P11.2) WILD-TYPE          3        1         0
D11V3, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              6                             2
  STAGE IA                             2                             2
  STAGE IB                             4                             2
  STAGE II                             1                             0
  STAGE IIA                           18                            17
  STAGE IIB                           19                             7
  STAGE III                           18                             5
  STAGE IIIA                           7                             4
  STAGE IIIB                           5                             3
  STAGE IIIC                           3                             3
  STAGE IV                             2                             1
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 11(7P11.2) MUTATED      18 15 55  2
  AMP PEAK 11(7P11.2) WILD-TYPE     8 18 19  2
D11V4, multiclass
       clus
vv      AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T0+T1                          18                             8
  T2                             15                            18
  T3                             55                            19
  T4                              2                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 11(7P11.2) MUTATED   40 40  6  3
  AMP PEAK 11(7P11.2) WILD-TYPE 24 14  5  3
D11V5, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  N0                          40                            24
  N1                          40                            14
  N2                           6                             5
  N3                           3                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK 11(7P11.2) MUTATED   70  1   3 12
  AMP PEAK 11(7P11.2) WILD-TYPE 41  1   0  5
D11V6, multiclass
     clus
vv    AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  M0                           70                            41
  M1                            1                             1
  M1A                           3                             0
  MX                           12                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   13 89
  AMP PEAK 11(7P11.2) WILD-TYPE  8 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     13   89
  AMP PEAK 11(7P11.2) WILD-TYPE    8   40
        clus
vv       AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  FEMALE                          13                             8
  MALE                            89                            40
[1] 2 2
[1] FALSE
D11V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7P11.2) MUTATED      26                         2    64
  AMP PEAK 11(7P11.2) WILD-TYPE    12                         0    29
D11V9, multiclass
                           clus
vv                          AMP PEAK 11(7P11.2) MUTATED
  ASIAN                                              26
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              64
                           clus
vv                          AMP PEAK 11(7P11.2) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(7Q21.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 12(7Q21.2) MUTATED   58 31
  AMP PEAK 12(7Q21.2) WILD-TYPE 30 23
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           89                            53 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           31                            23 
$`AMP PEAK 12(7Q21.2) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YB 
       31.27         8.94        16.24        32.45        20.09         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12         0.26         0.53        17.03        23.41         0.13 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
        0.43        44.75        60.39        68.02         3.68        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       15.48        23.18        25.28        18.08         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30         3.52         3.35        19.50         4.08        18.35 
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-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-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        12.92        16.47        13.55        13.22 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45         0.33         0.10         0.13         0.07         0.10 
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-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FW 
        0.07         0.07         0.10         0.20         1.18         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        8.02         7.59         7.04        29.59         6.35         9.30 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        7.00        14.01         5.29         3.42         8.48         8.15 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
       18.31         8.12        12.03         9.17        18.12 

$`AMP PEAK 12(7Q21.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT 
        4.21        33.27         0.85        20.78         0.03         0.99 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FG 
        0.79         0.36        14.86         0.46       122.10        41.52 
TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF 
       25.41        17.59         6.21         4.31         8.94         3.68 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
        8.78         6.41         7.17         7.43         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        7.40        55.50        13.48         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49W TCGA-LN-A4A5 
        8.71        83.24         0.16         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 
        0.07        17.62         5.16         5.06        14.70        53.95 
TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA7I 
        8.78         4.80         4.44        36.72        15.91 

  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                        68.02                        122.10 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                         7.04                          7.76 
[1] "0.1 - 68.0 (7.0)"  "0.0 - 122.1 (7.8)"
[1] "hr=" "1"  
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(7Q21.2) MUTATED         5        2        3        1        21
  AMP PEAK 12(7Q21.2) WILD-TYPE       3        2        3        0        14
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(7Q21.2) MUTATED          16        12          6          5
  AMP PEAK 12(7Q21.2) WILD-TYPE        10        11          5          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 12(7Q21.2) MUTATED            5        3         2
  AMP PEAK 12(7Q21.2) WILD-TYPE          1        0         0
D12V3, multiclass
            clus
vv           AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             2
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                           21                            14
  STAGE IIB                           16                            10
  STAGE III                           12                            11
  STAGE IIIA                           6                             5
  STAGE IIIB                           5                             3
  STAGE IIIC                           5                             1
  STAGE IV                             3                             0
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 12(7Q21.2) MUTATED      17 17 50  0
  AMP PEAK 12(7Q21.2) WILD-TYPE     9 16 24  4
D12V4, multiclass
       clus
vv      AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  T0+T1                          17                             9
  T2                             17                            16
  T3                             50                            24
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 12(7Q21.2) MUTATED   38 33  7  5
  AMP PEAK 12(7Q21.2) WILD-TYPE 26 21  4  1
D12V5, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  N0                          38                            26
  N1                          33                            21
  N2                           7                             4
  N3                           5                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK 12(7Q21.2) MUTATED   66  2   3 10
  AMP PEAK 12(7Q21.2) WILD-TYPE 45  0   0  7
D12V6, multiclass
     clus
vv    AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  M0                           66                            45
  M1                            2                             0
  M1A                           3                             0
  MX                           10                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                               cls
clus                             0  1
  AMP PEAK 12(7Q21.2) MUTATED   11 82
  AMP PEAK 12(7Q21.2) WILD-TYPE 10 47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     11   82
  AMP PEAK 12(7Q21.2) WILD-TYPE   10   47
        clus
vv       AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  FEMALE                          11                            10
  MALE                            82                            47
[1] 2 2
[1] FALSE
D12V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(7Q21.2) MUTATED      28                         2    56
  AMP PEAK 12(7Q21.2) WILD-TYPE    10                         0    37
D12V9, multiclass
                           clus
vv                          AMP PEAK 12(7Q21.2) MUTATED
  ASIAN                                              28
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              56
                           clus
vv                          AMP PEAK 12(7Q21.2) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(8P23.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 13(8P23.1) MUTATED   27 17
  AMP PEAK 13(8P23.1) WILD-TYPE 61 37
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           44                            98 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           17                            37 
$`AMP PEAK 13(8P23.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78        14.30         8.94        16.24        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A939 
       20.09        20.78         0.46       122.10        68.02        15.48 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.28        18.08        17.59         3.16         3.45         0.30 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OT 
        8.78         6.41         4.08        18.35         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM 
        7.13         0.36        55.50        12.92        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49U 
        5.42        21.37         8.71        10.36         0.07         0.07 
TCGA-LN-A49V TCGA-LN-A49X TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-RE-A7BO TCGA-V5-A7RE 
        0.10         0.10         7.59         5.06         7.00         4.80 
TCGA-V5-AASV TCGA-ZR-A9CJ 
        8.48        18.12 

$`AMP PEAK 13(8P23.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       31.27        58.55         7.63         5.92        13.94         4.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         0.43        44.75        60.39         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A43M 
       42.77        25.41        23.18         6.21         4.31         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-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        1.38        30.74        29.00         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.95         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NT 
       35.97        13.48        16.47        13.22        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        46.09        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y 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-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-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-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        3.78         8.02        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-A7RC 
       53.95         9.30         8.78        14.01         5.29         3.42 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.15         4.44        18.31         8.12        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I 
        9.17        15.91 

  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                        8.745                         6.990 
[1] "0.1 - 122.1 (8.7)" "0.0 - 83.2 (7.0)" 
[1] "hr=" "1.1"
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(8P23.1) MUTATED         3        2        2        0        10
  AMP PEAK 13(8P23.1) WILD-TYPE       5        2        4        1        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(8P23.1) MUTATED           8         6          2          1
  AMP PEAK 13(8P23.1) WILD-TYPE        18        17          9          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 13(8P23.1) MUTATED            4        2         1
  AMP PEAK 13(8P23.1) WILD-TYPE          2        1         1
D13V3, multiclass
            clus
vv           AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             2                             2
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                           10                            25
  STAGE IIB                            8                            18
  STAGE III                            6                            17
  STAGE IIIA                           2                             9
  STAGE IIIB                           1                             7
  STAGE IIIC                           4                             2
  STAGE IV                             2                             1
  STAGE IVA                            1                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 13(8P23.1) MUTATED      11  7 23  1
  AMP PEAK 13(8P23.1) WILD-TYPE    15 26 51  3
D13V4, multiclass
       clus
vv      AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  T0+T1                          11                            15
  T2                              7                            26
  T3                             23                            51
  T4                              1                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 13(8P23.1) MUTATED   22 15  1  4
  AMP PEAK 13(8P23.1) WILD-TYPE 42 39 10  2
D13V5, multiclass
    clus
vv   AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  N0                          22                            42
  N1                          15                            39
  N2                           1                            10
  N3                           4                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK 13(8P23.1) MUTATED   31  1   2  6
  AMP PEAK 13(8P23.1) WILD-TYPE 80  1   1 11
D13V6, multiclass
     clus
vv    AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  M0                           31                            80
  M1                            1                             1
  M1A                           2                             1
  MX                            6                            11
[1] 4 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(8P23.1) MUTATED   11 34
  AMP PEAK 13(8P23.1) WILD-TYPE 10 95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED     11   34
  AMP PEAK 13(8P23.1) WILD-TYPE   10   95
        clus
vv       AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  FEMALE                          11                            10
  MALE                            34                            95
[1] 2 2
[1] FALSE
D13V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8P23.1) MUTATED       7                         1    30
  AMP PEAK 13(8P23.1) WILD-TYPE    31                         1    63
D13V9, multiclass
                           clus
vv                          AMP PEAK 13(8P23.1) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              30
                           clus
vv                          AMP PEAK 13(8P23.1) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(8P11.21) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(8P11.21) MUTATED   42 26
  AMP PEAK 14(8P11.21) WILD-TYPE 46 28
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            68                             74 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            26                             28 
$`AMP PEAK 14(8P11.21) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30        58.55        13.94         8.94        16.24         4.21 
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        68.02 
TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
        3.68        23.18        25.28        17.59         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30         3.68         8.78         4.08        18.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A891 
        3.16         4.90         7.13         7.43         0.36         3.95 
TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       35.97        13.55        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        8.71        13.41        27.12        10.36         0.07        10.45 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
        0.13         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.10         0.10         0.07         0.10         7.59         5.06 
TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX 
       53.95         7.00         8.78        14.01         8.48         4.44 
TCGA-VR-A8EW TCGA-VR-AA7I 
        8.12        15.91 

$`AMP PEAK 14(8P11.21) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3Y9 
       25.78        31.27         7.63         5.92        32.45         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63        20.12         0.99         0.53         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
        0.13        14.86         0.43        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.48        18.08         6.21         4.31         8.94         3.52 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        3.35        19.50         6.41         7.17         1.38        30.74 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        46.09         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MR 
        0.10         0.07         0.13         0.10         0.07         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.20         1.18        17.62         5.16         3.78         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-V5-A7RB 
       14.70         7.04        29.59         6.35         9.30         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G 
        3.42         4.80         8.15        18.31        36.72        12.03 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                         7.675                          7.285 
[1] "0.0 - 122.1 (7.7)" "0.1 - 83.2 (7.3)" 
[1] "hr=" "1"  
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(8P11.21) MUTATED         4        2        2        1        15
  AMP PEAK 14(8P11.21) WILD-TYPE       4        2        4        0        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(8P11.21) MUTATED          14        14          2          5
  AMP PEAK 14(8P11.21) WILD-TYPE        12         9          9          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 14(8P11.21) MUTATED            4        1         1
  AMP PEAK 14(8P11.21) WILD-TYPE          2        2         1
D14V3, multiclass
            clus
vv           AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              2
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            15                             20
  STAGE IIB                            14                             12
  STAGE III                            14                              9
  STAGE IIIA                            2                              9
  STAGE IIIB                            5                              3
  STAGE IIIC                            4                              2
  STAGE IV                              1                              2
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 14(8P11.21) MUTATED      12 14 39  2
  AMP PEAK 14(8P11.21) WILD-TYPE    14 19 35  2
D14V4, multiclass
       clus
vv      AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  T0+T1                           12                             14
  T2                              14                             19
  T3                              39                             35
  T4                               2                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 14(8P11.21) MUTATED   31 27  5  4
  AMP PEAK 14(8P11.21) WILD-TYPE 33 27  6  2
D14V5, multiclass
    clus
vv   AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  N0                           31                             33
  N1                           27                             27
  N2                            5                              6
  N3                            4                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 14(8P11.21) MUTATED   55  0   2  7
  AMP PEAK 14(8P11.21) WILD-TYPE 56  2   1 10
D14V6, multiclass
     clus
vv    AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  M0                            55                             56
  M1                             0                              2
  M1A                            2                              1
  MX                             7                             10
[1] 4 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(8P11.21) MUTATED   10 62
  AMP PEAK 14(8P11.21) WILD-TYPE 11 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED     10   62
  AMP PEAK 14(8P11.21) WILD-TYPE   11   67
        clus
vv       AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  FEMALE                           10                             11
  MALE                             62                             67
[1] 2 2
[1] FALSE
D14V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(8P11.21) MUTATED      22                         1    41
  AMP PEAK 14(8P11.21) WILD-TYPE    16                         1    52
D14V9, multiclass
                           clus
vv                          AMP PEAK 14(8P11.21) MUTATED
  ASIAN                                               22
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               41
                           clus
vv                          AMP PEAK 14(8P11.21) WILD-TYPE
  ASIAN                                                 16
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(8Q24.21) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(8Q24.21) MUTATED   69 43
  AMP PEAK 15(8Q24.21) WILD-TYPE 19 11
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           112                             30 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                            43                             11 
$`AMP PEAK 15(8Q24.21) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
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-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.53        17.03         0.79         0.36         0.13         0.46 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.43       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       41.52        25.41        15.48        23.18        25.28        17.59 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OH 
        3.16         3.45         0.30         4.31         3.52        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        8.78         6.41         4.08        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        3.16        30.74         4.90         7.13         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK 
        0.36         3.95        55.50        35.97        12.92        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.42        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       27.12        46.09        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-A49V 
        0.07         0.33         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-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.10         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        1.18         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       29.59        53.95         7.00         8.78        14.01         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        4.80         8.48         8.15         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72         9.17        15.91        18.12 

$`AMP PEAK 15(8Q24.21) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-JY-A6FH TCGA-JY-A93E 
        0.03         0.99        23.41        14.86        42.77        18.08 
TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OP TCGA-L5-A4OU 
        6.21         8.94         3.68         3.35         7.17        29.00 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
        6.94         8.71        25.12         7.40         3.02         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A4A8 TCGA-M9-A5M8 
       13.48        16.47        83.24        52.57         0.07        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-V5-A7RC TCGA-VR-AA4G 
        5.16         3.78         6.35         9.30         3.42        12.03 

  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                         7.510                          8.055 
[1] "0.1 - 122.1 (7.5)" "0.0 - 83.2 (8.1)" 
[1] "hr=" "1.2"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(8Q24.21) MUTATED         6        2        5        1        27
  AMP PEAK 15(8Q24.21) WILD-TYPE       2        2        1        0         8
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(8Q24.21) MUTATED          21        21          8          6
  AMP PEAK 15(8Q24.21) WILD-TYPE         5         2          3          2
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 15(8Q24.21) MUTATED            6        3         1
  AMP PEAK 15(8Q24.21) WILD-TYPE          0        0         1
D15V3, multiclass
            clus
vv           AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  STAGE I                               6                              2
  STAGE IA                              2                              2
  STAGE IB                              5                              1
  STAGE II                              1                              0
  STAGE IIA                            27                              8
  STAGE IIB                            21                              5
  STAGE III                            21                              2
  STAGE IIIA                            8                              3
  STAGE IIIB                            6                              2
  STAGE IIIC                            6                              0
  STAGE IV                              3                              0
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 15(8Q24.21) MUTATED      19 27 61  3
  AMP PEAK 15(8Q24.21) WILD-TYPE     7  6 13  1
D15V4, multiclass
       clus
vv      AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  T0+T1                           19                              7
  T2                              27                              6
  T3                              61                             13
  T4                               3                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 15(8Q24.21) MUTATED   50 46  7  6
  AMP PEAK 15(8Q24.21) WILD-TYPE 14  8  4  0
D15V5, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  N0                           50                             14
  N1                           46                              8
  N2                            7                              4
  N3                            6                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 15(8Q24.21) MUTATED   91  2   2 12
  AMP PEAK 15(8Q24.21) WILD-TYPE 20  0   1  5
D15V6, multiclass
     clus
vv    AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  M0                            91                             20
  M1                             2                              0
  M1A                            2                              1
  MX                            12                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED    12 108
  AMP PEAK 15(8Q24.21) WILD-TYPE   9  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED     12  108
  AMP PEAK 15(8Q24.21) WILD-TYPE    9   21
        clus
vv       AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  FEMALE                           12                              9
  MALE                            108                             21
[1] 2 2
[1] FALSE
D15V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8Q24.21) MUTATED      37                         1    67
  AMP PEAK 15(8Q24.21) WILD-TYPE     1                         1    26
D15V9, multiclass
                           clus
vv                          AMP PEAK 15(8Q24.21) MUTATED
  ASIAN                                               37
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               67
                           clus
vv                          AMP PEAK 15(8Q24.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"

Clustering(16) Variable = AMP PEAK 16(9P13.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 16(9P13.3) MUTATED   16 12
  AMP PEAK 16(9P13.3) WILD-TYPE 72 42
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           28                           114 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           12                            42 
$`AMP PEAK 16(9P13.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FD 
       25.78        14.30         5.92         0.36       122.10        68.02 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU 
        0.30         4.31        19.50        18.35         3.16        29.00 
TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ 
        0.36        55.50        35.97        27.12        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A4MQ TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.07         0.33         0.10         3.78         5.06        14.70 
TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8Q7 TCGA-VR-AA7D 
       14.01         8.15        36.72         9.17 

$`AMP PEAK 16(9P13.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         0.13        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        0.43        44.75        60.39         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        6.21         3.16         3.45         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        3.35         8.78         6.41         4.08         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-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-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.42        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S 
       52.57        10.45         0.16         0.07         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-A4MR 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-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         7.04        29.59         6.35        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00         8.78         5.29         3.42         4.80         8.48 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7I TCGA-ZR-A9CJ 
        4.44        18.31         8.12        12.03        15.91        18.12 

  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                       12.185                         7.150 
[1] "0.1 - 122.1 (12.2)" "0.0 - 83.2 (7.2)"  
[1] "hr=" "1.3"
D16V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(9P13.3) MUTATED         2        1        2        0         6
  AMP PEAK 16(9P13.3) WILD-TYPE       6        3        4        1        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(9P13.3) MUTATED           4         7          1          2
  AMP PEAK 16(9P13.3) WILD-TYPE        22        16         10          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 16(9P13.3) MUTATED            2        0         0
  AMP PEAK 16(9P13.3) WILD-TYPE          4        3         2
D16V3, multiclass
            clus
vv           AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             3
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                            6                            29
  STAGE IIB                            4                            22
  STAGE III                            7                            16
  STAGE IIIA                           1                            10
  STAGE IIIB                           2                             6
  STAGE IIIC                           2                             4
  STAGE IV                             0                             3
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 16(9P13.3) MUTATED       5  4 19  0
  AMP PEAK 16(9P13.3) WILD-TYPE    21 29 55  4
D16V4, multiclass
       clus
vv      AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  T0+T1                           5                            21
  T2                              4                            29
  T3                             19                            55
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 16(9P13.3) MUTATED   13 11  2  2
  AMP PEAK 16(9P13.3) WILD-TYPE 51 43  9  4
D16V5, multiclass
    clus
vv   AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  N0                          13                            51
  N1                          11                            43
  N2                           2                             9
  N3                           2                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK 16(9P13.3) MUTATED   22  0   0  5
  AMP PEAK 16(9P13.3) WILD-TYPE 89  2   3 12
D16V6, multiclass
     clus
vv    AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  M0                           22                            89
  M1                            0                             2
  M1A                           0                             3
  MX                            5                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                               cls
clus                             0  1
  AMP PEAK 16(9P13.3) MUTATED    1 30
  AMP PEAK 16(9P13.3) WILD-TYPE 20 99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED      1   30
  AMP PEAK 16(9P13.3) WILD-TYPE   20   99
        clus
vv       AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  FEMALE                           1                            20
  MALE                            30                            99
[1] 2 2
[1] FALSE
D16V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(9P13.3) MUTATED       8                         0    19
  AMP PEAK 16(9P13.3) WILD-TYPE    30                         2    74
D16V9, multiclass
                           clus
vv                          AMP PEAK 16(9P13.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              19
                           clus
vv                          AMP PEAK 16(9P13.3) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(9Q34.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 17(9Q34.3) MUTATED   33 13
  AMP PEAK 17(9Q34.3) WILD-TYPE 55 41
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           46                            96 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           13                            41 
$`AMP PEAK 17(9Q34.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A6QS 
       31.27         5.92         4.21         0.53         0.36         0.13 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C 
        0.43       122.10        60.39         3.68        42.77        23.18 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW 
        3.16         4.31         3.32         1.38        29.00         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NL TCGA-L5-A8NS 
        2.60         0.36         3.95        55.50        13.22        13.41 
TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       27.12        46.09        10.36         0.07         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A9 
        0.10         0.10         0.10         0.13         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-S8-A6BV 
        0.10         0.20         8.02        14.70        53.95         8.78 
TCGA-S8-A6BW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
       14.01        36.72        12.03         9.17 

$`AMP PEAK 17(9Q34.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12         0.03         0.26         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD 
        0.79        23.41        14.86         0.46        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        25.41        15.48        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        6.21         3.45         0.30         8.94         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-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         3.16        30.74         4.90         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        8.71        25.12         7.40         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49L TCGA-LN-A49M 
       21.37         8.71        83.24        52.57        10.45         0.16 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 
        0.13         0.07         0.07         0.07         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.07         0.07         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        3.78         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        9.30         7.00         5.29         3.42         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.15         4.44        18.31         8.12        15.91        18.12 

  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                         4.26                          7.94 
[1] "0.1 - 122.1 (4.3)" "0.0 - 83.2 (7.9)" 
[1] "hr=" "1.5"
D17V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(9Q34.3) MUTATED         2        0        2        0        12
  AMP PEAK 17(9Q34.3) WILD-TYPE       6        4        4        1        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(9Q34.3) MUTATED          10         8          5          2
  AMP PEAK 17(9Q34.3) WILD-TYPE        16        15          6          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 17(9Q34.3) MUTATED            3        0         0
  AMP PEAK 17(9Q34.3) WILD-TYPE          3        3         2
D17V3, multiclass
            clus
vv           AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             4
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                           12                            23
  STAGE IIB                           10                            16
  STAGE III                            8                            15
  STAGE IIIA                           5                             6
  STAGE IIIB                           2                             6
  STAGE IIIC                           3                             3
  STAGE IV                             0                             3
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 17(9Q34.3) MUTATED       4 14 28  0
  AMP PEAK 17(9Q34.3) WILD-TYPE    22 19 46  4
D17V4, multiclass
       clus
vv      AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  T0+T1                           4                            22
  T2                             14                            19
  T3                             28                            46
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 17(9Q34.3) MUTATED   18 20  4  3
  AMP PEAK 17(9Q34.3) WILD-TYPE 46 34  7  3
D17V5, multiclass
    clus
vv   AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  N0                          18                            46
  N1                          20                            34
  N2                           4                             7
  N3                           3                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK 17(9Q34.3) MUTATED   39  0   0  7
  AMP PEAK 17(9Q34.3) WILD-TYPE 72  2   3 10
D17V6, multiclass
     clus
vv    AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  M0                           39                            72
  M1                            0                             2
  M1A                           0                             3
  MX                            7                            10
[1] 4 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(9Q34.3) MUTATED    2 48
  AMP PEAK 17(9Q34.3) WILD-TYPE 19 81
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED      2   48
  AMP PEAK 17(9Q34.3) WILD-TYPE   19   81
        clus
vv       AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  FEMALE                           2                            19
  MALE                            48                            81
[1] 2 2
[1] FALSE
D17V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(9Q34.3) MUTATED      19                         0    26
  AMP PEAK 17(9Q34.3) WILD-TYPE    19                         2    67
D17V9, multiclass
                           clus
vv                          AMP PEAK 17(9Q34.3) MUTATED
  ASIAN                                              19
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              26
                           clus
vv                          AMP PEAK 17(9Q34.3) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(11P13) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 18(11P13) MUTATED   21 19
  AMP PEAK 18(11P13) WILD-TYPE 67 35
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          40                          102 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          19                           35 
$`AMP PEAK 18(11P13) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A50L TCGA-IG-A97H 
       58.55         7.63         8.94        16.24         0.53         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OE 
      122.10         3.68        18.08         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-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV 
        3.95         2.66        13.48         5.42        27.12        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4MQ TCGA-LN-A4MR 
       46.09         0.07         0.13         0.10         0.10         0.07 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        3.78         8.02         7.59         7.04         6.35        53.95 
TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EU TCGA-ZR-A9CJ 
        7.00         3.42        18.31        18.12 

$`AMP PEAK 18(11P13) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       25.78        31.27        14.30         5.92        13.94         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         0.03         0.26         0.99        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA 
       23.41         0.36         0.13        14.86         0.46        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02        41.52        42.77        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        25.28        17.59         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
        4.31         3.68         3.35         8.78         6.41         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38         3.16        30.74         7.13         7.43 
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-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50        35.97        12.92        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.76        21.37         8.71        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.45         0.16         0.07         0.33         0.10         0.07 
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-A5U6 TCGA-LN-A5U7 
        0.10         0.10         0.07         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 
       17.62         5.16         5.06        14.70        29.59         9.30 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        8.78        14.01         5.29         4.80         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        4.44         8.12        36.72        12.03         9.17        15.91 

  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                      122.10                        83.24 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                        7.02                         7.94 
[1] "0.1 - 122.1 (7.0)" "0.0 - 83.2 (7.9)" 
[1] "hr=" "1.2"
D18V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(11P13) MUTATED         3        2        2        0        10
  AMP PEAK 18(11P13) WILD-TYPE       5        2        4        1        25
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(11P13) MUTATED           3         7          2          2
  AMP PEAK 18(11P13) WILD-TYPE        23        16          9          6
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(11P13) MUTATED            1        2         2
  AMP PEAK 18(11P13) WILD-TYPE          5        1         0
D18V3, multiclass
            clus
vv           AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  STAGE I                             3                            5
  STAGE IA                            2                            2
  STAGE IB                            2                            4
  STAGE II                            0                            1
  STAGE IIA                          10                           25
  STAGE IIB                           3                           23
  STAGE III                           7                           16
  STAGE IIIA                          2                            9
  STAGE IIIB                          2                            6
  STAGE IIIC                          1                            5
  STAGE IV                            2                            1
  STAGE IVA                           2                            0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 18(11P13) MUTATED       9  3 26  0
  AMP PEAK 18(11P13) WILD-TYPE    17 30 48  4
D18V4, multiclass
       clus
vv      AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  T0+T1                          9                           17
  T2                             3                           30
  T3                            26                           48
  T4                             0                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 18(11P13) MUTATED   17 16  3  1
  AMP PEAK 18(11P13) WILD-TYPE 47 38  8  5
D18V5, multiclass
    clus
vv   AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  N0                         17                           47
  N1                         16                           38
  N2                          3                            8
  N3                          1                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 M1A MX
  AMP PEAK 18(11P13) MUTATED   28  1   3  3
  AMP PEAK 18(11P13) WILD-TYPE 83  1   0 14
D18V6, multiclass
     clus
vv    AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  M0                          28                           83
  M1                           1                            1
  M1A                          3                            0
  MX                           3                           14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                              cls
clus                            0  1
  AMP PEAK 18(11P13) MUTATED    4 40
  AMP PEAK 18(11P13) WILD-TYPE 17 89
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(11P13) MUTATED      4   40
  AMP PEAK 18(11P13) WILD-TYPE   17   89
        clus
vv       AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  FEMALE                          4                           17
  MALE                           40                           89
[1] 2 2
[1] FALSE
D18V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(11P13) MUTATED      11                         1    27
  AMP PEAK 18(11P13) WILD-TYPE    27                         1    66
D18V9, multiclass
                           clus
vv                          AMP PEAK 18(11P13) MUTATED
  ASIAN                                             11
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             27
                           clus
vv                          AMP PEAK 18(11P13) WILD-TYPE
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = AMP PEAK 19(11P13) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 19(11P13) MUTATED   20 15
  AMP PEAK 19(11P13) WILD-TYPE 68 39
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          35                          107 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          15                           39 
$`AMP PEAK 19(11P13) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H 
        7.63         8.94        16.24         0.53         0.46         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OH 
      122.10         3.68        18.08         8.94         3.52        19.50 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NF 
        4.08        18.35         4.90        29.00         6.94         2.66 
TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S 
        5.42        27.12        52.57        46.09         0.07         0.13 
TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.10         0.10         0.10         0.07         3.78         7.59 
TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EU TCGA-ZR-A9CJ 
        7.04         7.00         3.42        18.31        18.12 

$`AMP PEAK 19(11P13) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12         0.03         0.26         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA 
        0.79        23.41         0.36         0.13        14.86        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02        41.52        42.77        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.28        17.59         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        0.30         4.31         3.68         3.35         8.78         6.41 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        3.32         7.17         1.38         3.16        30.74         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-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       13.41        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-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.13         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.20         1.18        17.62         5.16         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV 
       14.70        29.59         6.35        53.95         9.30         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       14.01         5.29         4.80         8.48         8.15         4.44 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.12        36.72        12.03         9.17        15.91 

  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                      122.10                        83.24 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                        6.94                         8.12 
[1] "0.1 - 122.1 (6.9)" "0.0 - 83.2 (8.1)" 
[1] "hr=" "1.3"
D19V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(11P13) MUTATED         2        1        2        0        12
  AMP PEAK 19(11P13) WILD-TYPE       6        3        4        1        23
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(11P13) MUTATED           3         6          2          3
  AMP PEAK 19(11P13) WILD-TYPE        23        17          9          5
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 19(11P13) MUTATED            1        2         2
  AMP PEAK 19(11P13) WILD-TYPE          5        1         0
D19V3, multiclass
            clus
vv           AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  STAGE I                             2                            6
  STAGE IA                            1                            3
  STAGE IB                            2                            4
  STAGE II                            0                            1
  STAGE IIA                          12                           23
  STAGE IIB                           3                           23
  STAGE III                           6                           17
  STAGE IIIA                          2                            9
  STAGE IIIB                          3                            5
  STAGE IIIC                          1                            5
  STAGE IV                            2                            1
  STAGE IVA                           2                            0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 19(11P13) MUTATED       7  5 25  0
  AMP PEAK 19(11P13) WILD-TYPE    19 28 49  4
D19V4, multiclass
       clus
vv      AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  T0+T1                          7                           19
  T2                             5                           28
  T3                            25                           49
  T4                             0                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 19(11P13) MUTATED   17 14  4  1
  AMP PEAK 19(11P13) WILD-TYPE 47 40  7  5
D19V5, multiclass
    clus
vv   AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  N0                         17                           47
  N1                         14                           40
  N2                          4                            7
  N3                          1                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 M1A MX
  AMP PEAK 19(11P13) MUTATED   27  1   3  3
  AMP PEAK 19(11P13) WILD-TYPE 84  1   0 14
D19V6, multiclass
     clus
vv    AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  M0                          27                           84
  M1                           1                            1
  M1A                          3                            0
  MX                           3                           14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                              cls
clus                            0  1
  AMP PEAK 19(11P13) MUTATED    4 36
  AMP PEAK 19(11P13) WILD-TYPE 17 93
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED      4   36
  AMP PEAK 19(11P13) WILD-TYPE   17   93
        clus
vv       AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  FEMALE                          4                           17
  MALE                           36                           93
[1] 2 2
[1] FALSE
D19V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(11P13) MUTATED      14                         1    21
  AMP PEAK 19(11P13) WILD-TYPE    24                         1    72
D19V9, multiclass
                           clus
vv                          AMP PEAK 19(11P13) MUTATED
  ASIAN                                             14
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             21
                           clus
vv                          AMP PEAK 19(11P13) WILD-TYPE
  ASIAN                                               24
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(11Q13.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(11Q13.3) MUTATED   50 25
  AMP PEAK 20(11Q13.3) WILD-TYPE 38 29
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            75                             67 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            25                             29 
$`AMP PEAK 20(11Q13.3) MUTATED`
TCGA-2H-A9GN TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
        8.94        33.27         0.85        20.78        20.12         0.03 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       17.03        23.41         0.13         0.46         0.43       122.10 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J 
       60.39         3.68        25.41        18.08         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM 
        8.94         3.52         3.68         3.35        19.50         4.08 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
        1.38        30.74        29.00         6.94         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        3.95        55.50         2.66        12.92        13.48        13.55 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
        5.42        21.37         8.71        52.57        46.09         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
        0.16         0.07         0.10         0.13         0.10         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-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        3.78         8.02         7.59         7.04         6.35        53.95 
TCGA-RE-A7BO TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G 
        7.00         3.42         8.15        18.31         8.12        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

$`AMP PEAK 20(11Q13.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YB 
       13.94        16.24         4.21        32.45        20.09         2.63 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP 
        0.26         0.99         0.53         0.79         0.36        14.86 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        42.77        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OI 
       25.28        17.59         6.21         3.16         3.45         8.78 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT 
        6.41        18.35         3.32         7.17         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        7.13         7.43         8.71        25.12         7.40         3.02 
TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NS TCGA-L5-A8NT 
       35.97        16.47        13.22         7.76        13.41        27.12 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A4A9 
       83.24        10.36        10.45         0.33         0.07         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 
       17.62         5.16         5.06        14.70        29.59         9.30 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        8.78        14.01         5.29         4.80         8.48         4.44 
TCGA-VR-A8Q7 
       36.72 

  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                          4.31                           8.78 
[1] "0.0 - 122.1 (4.3)" "0.1 - 83.2 (8.8)" 
[1] "hr=" "1"  
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(11Q13.3) MUTATED         4        1        2        1        22
  AMP PEAK 20(11Q13.3) WILD-TYPE       4        3        4        0        13
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(11Q13.3) MUTATED          12        14          6          4
  AMP PEAK 20(11Q13.3) WILD-TYPE        14         9          5          4
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 20(11Q13.3) MUTATED            2        2         1
  AMP PEAK 20(11Q13.3) WILD-TYPE          4        1         1
D20V3, multiclass
            clus
vv           AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              3
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            22                             13
  STAGE IIB                            12                             14
  STAGE III                            14                              9
  STAGE IIIA                            6                              5
  STAGE IIIB                            4                              4
  STAGE IIIC                            2                              4
  STAGE IV                              2                              1
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 20(11Q13.3) MUTATED      12 20 39  3
  AMP PEAK 20(11Q13.3) WILD-TYPE    14 13 35  1
D20V4, multiclass
       clus
vv      AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  T0+T1                           12                             14
  T2                              20                             13
  T3                              39                             35
  T4                               3                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 20(11Q13.3) MUTATED   37 27  7  2
  AMP PEAK 20(11Q13.3) WILD-TYPE 27 27  4  4
D20V5, multiclass
    clus
vv   AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  N0                           37                             27
  N1                           27                             27
  N2                            7                              4
  N3                            2                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 20(11Q13.3) MUTATED   61  2   1  7
  AMP PEAK 20(11Q13.3) WILD-TYPE 50  0   2 10
D20V6, multiclass
     clus
vv    AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  M0                            61                             50
  M1                             2                              0
  M1A                            1                              2
  MX                             7                             10
[1] 4 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(11Q13.3) MUTATED   11 70
  AMP PEAK 20(11Q13.3) WILD-TYPE 10 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     11   70
  AMP PEAK 20(11Q13.3) WILD-TYPE   10   59
        clus
vv       AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  FEMALE                           11                             10
  MALE                             70                             59
[1] 2 2
[1] FALSE
D20V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(11Q13.3) MUTATED      27                         1    49
  AMP PEAK 20(11Q13.3) WILD-TYPE    11                         1    44
D20V9, multiclass
                           clus
vv                          AMP PEAK 20(11Q13.3) MUTATED
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               49
                           clus
vv                          AMP PEAK 20(11Q13.3) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(12P12.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 21(12P12.1) MUTATED   36 22
  AMP PEAK 21(12P12.1) WILD-TYPE 52 32
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            58                             84 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            22                             32 
$`AMP PEAK 21(12P12.1) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
        7.63         5.92        16.24         4.21        32.45        20.09 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 
        2.63        20.12         0.03         0.26         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A93D TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI 
        0.43        25.28         0.30         4.31         3.52         8.78 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S 
        4.08        18.35         3.32         4.90        29.00         6.94 
TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NT 
        0.36         2.66        16.47        13.22        21.37        27.12 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       46.09        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 TCGA-VR-A8EU TCGA-VR-A8EW TCGA-ZR-A9CJ 
       14.01        18.31         8.12        18.12 

$`AMP PEAK 21(12P12.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55        13.94         8.94 
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        14.86         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        23.18        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.45         8.94         3.68         3.35        19.50         6.41 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38         3.16        30.74         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-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM 
       55.50        35.97        12.92        13.48        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49N 
        5.42         8.71        13.41        83.24        52.57         0.07 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 
        0.07         0.10         0.07         0.13         0.10         0.07 
TCGA-LN-A4MQ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.10        17.62         5.16         3.78        14.70         7.04 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        9.30         7.00         5.29         3.42         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.15         4.44        36.72        12.03         9.17        15.91 

  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                         53.95                         122.10 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                         5.490                          8.595 
[1] "0.0 - 54.0 (5.5)"  "0.1 - 122.1 (8.6)"
[1] "hr=" "1.5"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(12P12.1) MUTATED         0        1        3        1        18
  AMP PEAK 21(12P12.1) WILD-TYPE       8        3        3        0        17
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(12P12.1) MUTATED           7        10          4          3
  AMP PEAK 21(12P12.1) WILD-TYPE        19        13          7          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(12P12.1) MUTATED            5        2         2
  AMP PEAK 21(12P12.1) WILD-TYPE          1        1         0
D21V3, multiclass
            clus
vv           AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  STAGE I                               0                              8
  STAGE IA                              1                              3
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                            18                             17
  STAGE IIB                             7                             19
  STAGE III                            10                             13
  STAGE IIIA                            4                              7
  STAGE IIIB                            3                              5
  STAGE IIIC                            5                              1
  STAGE IV                              2                              1
  STAGE IVA                             2                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 21(12P12.1) MUTATED       5 15 37  0
  AMP PEAK 21(12P12.1) WILD-TYPE    21 18 37  4
D21V4, multiclass
       clus
vv      AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  T0+T1                            5                             21
  T2                              15                             18
  T3                              37                             37
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 21(12P12.1) MUTATED   27 21  3  5
  AMP PEAK 21(12P12.1) WILD-TYPE 37 33  8  1
D21V5, multiclass
    clus
vv   AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  N0                           27                             37
  N1                           21                             33
  N2                            3                              8
  N3                            5                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 21(12P12.1) MUTATED   42  1   3  8
  AMP PEAK 21(12P12.1) WILD-TYPE 69  1   0  9
D21V6, multiclass
     clus
vv    AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  M0                            42                             69
  M1                             1                              1
  M1A                            3                              0
  MX                             8                              9
[1] 4 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(12P12.1) MUTATED    3 60
  AMP PEAK 21(12P12.1) WILD-TYPE 18 69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(12P12.1) MUTATED      3   60
  AMP PEAK 21(12P12.1) WILD-TYPE   18   69
        clus
vv       AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  FEMALE                            3                             18
  MALE                             60                             69
[1] 2 2
[1] FALSE
D21V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(12P12.1) MUTATED      23                         0    35
  AMP PEAK 21(12P12.1) WILD-TYPE    15                         2    58
D21V9, multiclass
                           clus
vv                          AMP PEAK 21(12P12.1) MUTATED
  ASIAN                                               23
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               35
                           clus
vv                          AMP PEAK 21(12P12.1) WILD-TYPE
  ASIAN                                                 15
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(12Q15) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 22(12Q15) MUTATED   24 13
  AMP PEAK 22(12Q15) WILD-TYPE 64 41
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          37                          105 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          13                           41 
$`AMP PEAK 22(12Q15) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A43J 
        7.63        16.24        32.45         0.53         0.46         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT 
        8.94         3.52         6.41         4.08         3.32         4.90 
TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN 
        6.94        55.50         2.66        13.48        13.22         5.42 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V 
       27.12        52.57        46.09        10.36        10.45         0.10 
TCGA-LN-A49W TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.07         0.10         0.10         0.07         0.07         0.10 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8Q7 
        7.59        29.59         6.35        14.01         3.42        36.72 
TCGA-ZR-A9CJ 
       18.12 

$`AMP PEAK 22(12Q15) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94         4.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12         0.03         0.26         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.79        23.41         0.36         0.13        14.86         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        15.48        23.18        25.28        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       17.59         6.21         3.16         3.45         0.30         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        3.35        19.50         8.78        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        3.16        30.74        29.00         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-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
       35.97        12.92        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
        8.71        13.41        83.24         0.07         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
        0.33         0.10         0.13         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.13         0.07         0.10         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       17.62         5.16         3.78         8.02         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        7.04        53.95         9.30         7.00         8.78         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        4.80         8.48         8.15         4.44        18.31         8.12 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.03         9.17        15.91 

  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                        55.5                        122.1 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                        6.41                         8.02 
[1] "0.1 - 55.5 (6.4)"  "0.0 - 122.1 (8.0)"
[1] "hr=" "1"  
D22V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(12Q15) MUTATED         1        1        3        1         7
  AMP PEAK 22(12Q15) WILD-TYPE       7        3        3        0        28
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(12Q15) MUTATED           3         7          2          2
  AMP PEAK 22(12Q15) WILD-TYPE        23        16          9          6
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(12Q15) MUTATED            3        1         2
  AMP PEAK 22(12Q15) WILD-TYPE          3        2         0
D22V3, multiclass
            clus
vv           AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  STAGE I                             1                            7
  STAGE IA                            1                            3
  STAGE IB                            3                            3
  STAGE II                            1                            0
  STAGE IIA                           7                           28
  STAGE IIB                           3                           23
  STAGE III                           7                           16
  STAGE IIIA                          2                            9
  STAGE IIIB                          2                            6
  STAGE IIIC                          3                            3
  STAGE IV                            1                            2
  STAGE IVA                           2                            0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 22(12Q15) MUTATED       3  7 24  0
  AMP PEAK 22(12Q15) WILD-TYPE    23 26 50  4
D22V4, multiclass
       clus
vv      AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  T0+T1                          3                           23
  T2                             7                           26
  T3                            24                           50
  T4                             0                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 22(12Q15) MUTATED   15 13  3  3
  AMP PEAK 22(12Q15) WILD-TYPE 49 41  8  3
D22V5, multiclass
    clus
vv   AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  N0                         15                           49
  N1                         13                           41
  N2                          3                            8
  N3                          3                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 M1A MX
  AMP PEAK 22(12Q15) MUTATED   23  0   3  6
  AMP PEAK 22(12Q15) WILD-TYPE 88  2   0 11
D22V6, multiclass
     clus
vv    AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  M0                          23                           88
  M1                           0                            2
  M1A                          3                            0
  MX                           6                           11
[1] 4 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(12Q15) MUTATED    4 34
  AMP PEAK 22(12Q15) WILD-TYPE 17 95
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(12Q15) MUTATED      4   34
  AMP PEAK 22(12Q15) WILD-TYPE   17   95
        clus
vv       AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  FEMALE                          4                           17
  MALE                           34                           95
[1] 2 2
[1] FALSE
D22V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(12Q15) MUTATED      11                         1    22
  AMP PEAK 22(12Q15) WILD-TYPE    27                         1    71
D22V9, multiclass
                           clus
vv                          AMP PEAK 22(12Q15) MUTATED
  ASIAN                                             11
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             22
                           clus
vv                          AMP PEAK 22(12Q15) WILD-TYPE
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(13Q22.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 23(13Q22.1) MUTATED   35 18
  AMP PEAK 23(13Q22.1) WILD-TYPE 53 36
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            53                             89 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            18                             36 
$`AMP PEAK 23(13Q22.1) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A50L 
       31.27        14.30         5.92        13.94         4.21         0.53 
TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C 
        0.79         0.43       122.10         3.68        42.77        23.18 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       25.28         3.16         3.45         8.94         3.35         8.78 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        7.17         1.38        30.74         7.13         6.94         0.36 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NR 
        3.02        55.50         2.66        12.92        13.55         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49U 
       13.41        27.12        46.09        10.45         0.10         0.07 
TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-Q9-A6FW 
        0.10         0.10         0.10         0.10         1.18         3.78 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02        14.70         7.04        29.59        53.95         9.30 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-ZR-A9CJ 
        8.78         5.29         3.42         8.15        18.12 

$`AMP PEAK 23(13Q22.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        58.55         7.63         8.94        16.24        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        0.03         0.26         0.99        17.03        23.41         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13        14.86         0.46        44.75        60.39        68.02 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        25.41        15.48        18.08        17.59         6.21 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        0.30         4.31         3.52         3.68        19.50         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        4.08        18.35         3.32         3.16         4.90        29.00 
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-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        13.48        16.47        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       21.37        83.24        52.57        10.36         0.07         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.07         0.33         0.13         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.13         0.07         0.10         0.07         0.07         0.07 
TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ 
        0.20        17.62         5.16         7.59         5.06         6.35 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU 
        7.00        14.01         4.80         8.48         4.44        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.12        36.72        12.03         9.17        15.91 

  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                          7.17                           7.59 
[1] "0.1 - 122.1 (7.2)" "0.0 - 83.2 (7.6)" 
[1] "hr=" "1.2"
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(13Q22.1) MUTATED         4        1        3        1         9
  AMP PEAK 23(13Q22.1) WILD-TYPE       4        3        3        0        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(13Q22.1) MUTATED           8         8          3          2
  AMP PEAK 23(13Q22.1) WILD-TYPE        18        15          8          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(13Q22.1) MUTATED            3        1         1
  AMP PEAK 23(13Q22.1) WILD-TYPE          3        2         1
D23V3, multiclass
            clus
vv           AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              3
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                             9                             26
  STAGE IIB                             8                             18
  STAGE III                             8                             15
  STAGE IIIA                            3                              8
  STAGE IIIB                            2                              6
  STAGE IIIC                            3                              3
  STAGE IV                              1                              2
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 23(13Q22.1) MUTATED      11 12 24  0
  AMP PEAK 23(13Q22.1) WILD-TYPE    15 21 50  4
D23V4, multiclass
       clus
vv      AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  T0+T1                           11                             15
  T2                              12                             21
  T3                              24                             50
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 23(13Q22.1) MUTATED   21 18  4  3
  AMP PEAK 23(13Q22.1) WILD-TYPE 43 36  7  3
D23V5, multiclass
    clus
vv   AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  N0                           21                             43
  N1                           18                             36
  N2                            4                              7
  N3                            3                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 23(13Q22.1) MUTATED   36  1   1  9
  AMP PEAK 23(13Q22.1) WILD-TYPE 75  1   2  8
D23V6, multiclass
     clus
vv    AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  M0                            36                             75
  M1                             1                              1
  M1A                            1                              2
  MX                             9                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                              0  1
  AMP PEAK 23(13Q22.1) MUTATED    8 48
  AMP PEAK 23(13Q22.1) WILD-TYPE 13 81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(13Q22.1) MUTATED      8   48
  AMP PEAK 23(13Q22.1) WILD-TYPE   13   81
        clus
vv       AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  FEMALE                            8                             13
  MALE                             48                             81
[1] 2 2
[1] FALSE
D23V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(13Q22.1) MUTATED      14                         1    32
  AMP PEAK 23(13Q22.1) WILD-TYPE    24                         1    61
D23V9, multiclass
                           clus
vv                          AMP PEAK 23(13Q22.1) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               32
                           clus
vv                          AMP PEAK 23(13Q22.1) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(14Q21.1) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 24(14Q21.1) MUTATED   25 16
  AMP PEAK 24(14Q21.1) WILD-TYPE 63 38
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            41                            101 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            16                             38 
$`AMP PEAK 24(14Q21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
       25.78         5.92        32.45         0.85        20.78         0.03 
TCGA-IG-A50L TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43C 
        0.53         0.13         0.46        42.77        23.18         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A8NG TCGA-L5-A8NN 
        3.45         4.31         3.16         7.43        35.97         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S 
       21.37        13.41         0.07        10.45         0.33         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW 
        0.20         8.02        29.59        53.95         8.78        14.01 
TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        4.44         8.12         9.17        15.91        18.12 

$`AMP PEAK 24(14Q21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC 
       16.24         4.21        33.27        20.09         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        0.26         0.99        17.03         0.79        23.41         0.36 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         0.43       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        25.41        15.48        25.28        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       17.59         6.21         0.30         8.94         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-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.95         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR 
       13.48        16.47        13.55        13.22         7.76         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M 
       27.12        83.24        52.57        46.09        10.36         0.16 
TCGA-LN-A49N TCGA-LN-A49R 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-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.10         0.07         0.10         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-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        6.35         9.30         7.00         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.48         8.15        18.31        36.72        12.03 

  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                         53.95                         122.10 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                          5.42                           7.76 
[1] "0.0 - 54.0 (5.4)"  "0.1 - 122.1 (7.8)"
[1] "hr=" "1.4"
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(14Q21.1) MUTATED         1        1        1        0        15
  AMP PEAK 24(14Q21.1) WILD-TYPE       7        3        5        1        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(14Q21.1) MUTATED           7         7          4          3
  AMP PEAK 24(14Q21.1) WILD-TYPE        19        16          7          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 24(14Q21.1) MUTATED            2        0         0
  AMP PEAK 24(14Q21.1) WILD-TYPE          4        3         2
D24V3, multiclass
            clus
vv           AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              1                              3
  STAGE IB                              1                              5
  STAGE II                              0                              1
  STAGE IIA                            15                             20
  STAGE IIB                             7                             19
  STAGE III                             7                             16
  STAGE IIIA                            4                              7
  STAGE IIIB                            3                              5
  STAGE IIIC                            2                              4
  STAGE IV                              0                              3
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 24(14Q21.1) MUTATED       2 14 22  3
  AMP PEAK 24(14Q21.1) WILD-TYPE    24 19 52  1
D24V4, multiclass
       clus
vv      AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  T0+T1                            2                             24
  T2                              14                             19
  T3                              22                             52
  T4                               3                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 24(14Q21.1) MUTATED   23 13  3  2
  AMP PEAK 24(14Q21.1) WILD-TYPE 41 41  8  4
D24V5, multiclass
    clus
vv   AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  N0                           23                             41
  N1                           13                             41
  N2                            3                              8
  N3                            2                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 24(14Q21.1) MUTATED   36  0   0  5
  AMP PEAK 24(14Q21.1) WILD-TYPE 75  2   3 12
D24V6, multiclass
     clus
vv    AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  M0                            36                             75
  M1                             0                              2
  M1A                            0                              3
  MX                             5                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                cls
clus                              0  1
  AMP PEAK 24(14Q21.1) MUTATED    0 46
  AMP PEAK 24(14Q21.1) WILD-TYPE 21 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(14Q21.1) MUTATED      0   46
  AMP PEAK 24(14Q21.1) WILD-TYPE   21   83
        clus
vv       AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  FEMALE                            0                             21
  MALE                             46                             83
[1] 2 2
[1] FALSE
D24V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(14Q21.1) MUTATED      19                         0    23
  AMP PEAK 24(14Q21.1) WILD-TYPE    19                         2    70
D24V9, multiclass
                           clus
vv                          AMP PEAK 24(14Q21.1) MUTATED
  ASIAN                                               19
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               23
                           clus
vv                          AMP PEAK 24(14Q21.1) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = AMP PEAK 25(15Q26.1) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 25(15Q26.1) MUTATED   27 19
  AMP PEAK 25(15Q26.1) WILD-TYPE 61 35
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            46                             96 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            19                             35 
$`AMP PEAK 25(15Q26.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A50L 
       25.78        58.55         7.63         8.94        32.45         0.53 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43M 
      122.10        60.39         3.68        42.77         3.16         8.94 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        4.08         7.17         1.38         3.16        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
       29.00         7.13         6.94         2.60         0.36         3.95 
TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A6VZ 
       55.50        16.47        21.37        13.41        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       10.45         0.10         0.10         0.07        17.62         3.78 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04         6.35        53.95         9.30 
TCGA-S8-A6BW TCGA-VR-A8EU TCGA-VR-AA7D TCGA-ZR-A9CJ 
       14.01        18.31         9.17        18.12 

$`AMP PEAK 25(15Q26.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-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-A5S3 
        0.03         0.26         0.99        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA 
        0.36         0.13        14.86         0.46         0.43        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02        41.52        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       18.08        17.59         6.21         3.45         0.30         4.31 
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-A4ON TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       18.35         3.32         7.43         8.71        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        3.02         2.66        35.97        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22         7.76         5.42         8.71        27.12        83.24 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       52.57         0.07         0.16         0.07         0.33         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-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.07         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG 
        0.20         1.18         5.16         8.02         5.06        29.59 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00         8.78         5.29         3.42         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I 
        8.15         4.44         8.12        36.72        12.03        15.91 

  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                         9.055                          6.310 
[1] "0.1 - 122.1 (9.1)" "0.0 - 83.2 (6.3)" 
[1] "hr=" "1.3"
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(15Q26.1) MUTATED         3        3        3        0        10
  AMP PEAK 25(15Q26.1) WILD-TYPE       5        1        3        1        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(15Q26.1) MUTATED           5         7          2          1
  AMP PEAK 25(15Q26.1) WILD-TYPE        21        16          9          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 25(15Q26.1) MUTATED            3        2         0
  AMP PEAK 25(15Q26.1) WILD-TYPE          3        1         2
D25V3, multiclass
            clus
vv           AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              3                              1
  STAGE IB                              3                              3
  STAGE II                              0                              1
  STAGE IIA                            10                             25
  STAGE IIB                             5                             21
  STAGE III                             7                             16
  STAGE IIIA                            2                              9
  STAGE IIIB                            1                              7
  STAGE IIIC                            3                              3
  STAGE IV                              2                              1
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 25(15Q26.1) MUTATED       8 14 20  0
  AMP PEAK 25(15Q26.1) WILD-TYPE    18 19 54  4
D25V4, multiclass
       clus
vv      AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  T0+T1                            8                             18
  T2                              14                             19
  T3                              20                             54
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 25(15Q26.1) MUTATED   20 16  3  3
  AMP PEAK 25(15Q26.1) WILD-TYPE 44 38  8  3
D25V5, multiclass
    clus
vv   AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  N0                           20                             44
  N1                           16                             38
  N2                            3                              8
  N3                            3                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 25(15Q26.1) MUTATED   29  1   1 10
  AMP PEAK 25(15Q26.1) WILD-TYPE 82  1   2  7
D25V6, multiclass
     clus
vv    AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  M0                            29                             82
  M1                             1                              1
  M1A                            1                              2
  MX                            10                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                                cls
clus                              0  1
  AMP PEAK 25(15Q26.1) MUTATED    6 43
  AMP PEAK 25(15Q26.1) WILD-TYPE 15 86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(15Q26.1) MUTATED      6   43
  AMP PEAK 25(15Q26.1) WILD-TYPE   15   86
        clus
vv       AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  FEMALE                            6                             15
  MALE                             43                             86
[1] 2 2
[1] FALSE
D25V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(15Q26.1) MUTATED       8                         0    32
  AMP PEAK 25(15Q26.1) WILD-TYPE    30                         2    61
D25V9, multiclass
                           clus
vv                          AMP PEAK 25(15Q26.1) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               32
                           clus
vv                          AMP PEAK 25(15Q26.1) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = AMP PEAK 26(17Q12) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 26(17Q12) MUTATED   38 21
  AMP PEAK 26(17Q12) WILD-TYPE 50 33
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          59                           83 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          21                           33 
$`AMP PEAK 26(17Q12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A3QL 
       25.78        14.30        58.55        13.94         8.94        20.09 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93C 
        0.53        17.03         0.36        60.39        25.41        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4ON 
       25.28        18.08         3.45         0.30         3.52        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         1.38        30.74         4.90        29.00         7.13 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        2.60         7.40        35.97        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT TCGA-LN-A49L TCGA-LN-A49R 
       13.22         5.42         8.71        27.12        10.45         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.13         0.07         0.10         0.13         0.07         0.10 
TCGA-LN-A4A8 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07        17.62         3.78         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        7.04        29.59        53.95        14.01         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-AA7I 
        8.48         8.15         4.44        18.31        15.91 

$`AMP PEAK 26(17Q12) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
       31.27         7.63         5.92        16.24         4.21        32.45 
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-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.26         0.99         0.79        23.41         0.13        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        0.46         0.43       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       41.52        42.77        15.48        17.59         6.21         3.16 
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-A4OP TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A88S 
        6.41         4.08         7.17         3.16         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        8.71        25.12         0.36         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
        2.66        13.55         7.76        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.36         0.07         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.33         0.07         0.10         0.07         0.10         0.10 
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-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       14.70         6.35         9.30         7.00         8.78         5.29 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
        8.12        36.72        12.03         9.17        18.12 

  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                       60.39                       122.10 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                        8.48                         6.94 
[1] "0.1 - 60.4 (8.5)"  "0.0 - 122.1 (6.9)"
[1] "hr=" "1.2"
D26V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(17Q12) MUTATED         3        0        2        0        10
  AMP PEAK 26(17Q12) WILD-TYPE       5        4        4        1        25
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(17Q12) MUTATED           9        15          3          4
  AMP PEAK 26(17Q12) WILD-TYPE        17         8          8          4
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 26(17Q12) MUTATED            2        3         0
  AMP PEAK 26(17Q12) WILD-TYPE          4        0         2
D26V3, multiclass
            clus
vv           AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  STAGE I                             3                            5
  STAGE IA                            0                            4
  STAGE IB                            2                            4
  STAGE II                            0                            1
  STAGE IIA                          10                           25
  STAGE IIB                           9                           17
  STAGE III                          15                            8
  STAGE IIIA                          3                            8
  STAGE IIIB                          4                            4
  STAGE IIIC                          2                            4
  STAGE IV                            3                            0
  STAGE IVA                           0                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 26(17Q12) MUTATED      10  8 32  1
  AMP PEAK 26(17Q12) WILD-TYPE    16 25 42  3
D26V4, multiclass
       clus
vv      AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  T0+T1                         10                           16
  T2                             8                           25
  T3                            32                           42
  T4                             1                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 26(17Q12) MUTATED   20 24  5  2
  AMP PEAK 26(17Q12) WILD-TYPE 44 30  6  4
D26V5, multiclass
    clus
vv   AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  N0                         20                           44
  N1                         24                           30
  N2                          5                            6
  N3                          2                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 M1A MX
  AMP PEAK 26(17Q12) MUTATED   42  2   1  4
  AMP PEAK 26(17Q12) WILD-TYPE 69  0   2 13
D26V6, multiclass
     clus
vv    AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  M0                          42                           69
  M1                           2                            0
  M1A                          1                            2
  MX                           4                           13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                              cls
clus                            0  1
  AMP PEAK 26(17Q12) MUTATED    5 55
  AMP PEAK 26(17Q12) WILD-TYPE 16 74
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(17Q12) MUTATED      5   55
  AMP PEAK 26(17Q12) WILD-TYPE   16   74
        clus
vv       AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  FEMALE                          5                           16
  MALE                           55                           74
[1] 2 2
[1] FALSE
D26V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(17Q12) MUTATED      13                         2    37
  AMP PEAK 26(17Q12) WILD-TYPE    25                         0    56
D26V9, multiclass
                           clus
vv                          AMP PEAK 26(17Q12) MUTATED
  ASIAN                                             13
  BLACK OR AFRICAN AMERICAN                          2
  WHITE                                             37
                           clus
vv                          AMP PEAK 26(17Q12) WILD-TYPE
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = AMP PEAK 27(18P11.32) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 27(18P11.32) MUTATED   31 20
  AMP PEAK 27(18P11.32) WILD-TYPE 57 34
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             51                              91 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             20                              34 
$`AMP PEAK 27(18P11.32) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A50L 
        7.63        13.94        16.24         4.21        32.45         0.53 
TCGA-IG-A625 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A938 
        0.36         0.43        44.75        60.39         3.68        25.41 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ 
        3.16         4.31         8.94         4.08         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NF 
        3.16         4.90         7.13         2.60         0.36         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT 
       13.48        16.47        13.22         5.42        21.37        27.12 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       46.09        10.36         0.33         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4MQ 
        0.07         0.10         0.07         0.07         0.10         0.10 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RC 
        0.07         1.18         5.06        53.95        14.01         3.42 
TCGA-V5-A7RE TCGA-VR-A8Q7 TCGA-VR-AA7D 
        4.80        36.72         9.17 

$`AMP PEAK 27(18P11.32) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55         5.92         8.94 
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-A5S3 
        0.03         0.26         0.99        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG 
        0.13        14.86         0.46       122.10        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        15.48        23.18        25.28        18.08        17.59 
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-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK 
        3.95         3.02        55.50        35.97        12.92        13.55 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K 
        7.76         8.71        13.41        83.24        52.57         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A4A2 TCGA-LN-A4A5 
       10.45         0.16         0.07         0.10         0.13         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.07         0.07         0.20        17.62         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-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV 
        6.35         9.30         7.00         8.78         5.29         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7I 
        8.15         4.44        18.31         8.12        12.03        15.91 
TCGA-ZR-A9CJ 
       18.12 

  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                           0.07                            0.03 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                          60.39                          122.10 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                           4.21                            8.71 
[1] "0.1 - 60.4 (4.2)"  "0.0 - 122.1 (8.7)"
[1] "hr=" "1.5"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(18P11.32) MUTATED         1        2        3        0        14
  AMP PEAK 27(18P11.32) WILD-TYPE       7        2        3        1        21
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(18P11.32) MUTATED           6        13          3          1
  AMP PEAK 27(18P11.32) WILD-TYPE        20        10          8          7
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 27(18P11.32) MUTATED            3        1         2
  AMP PEAK 27(18P11.32) WILD-TYPE          3        2         0
D27V3, multiclass
            clus
vv           AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  STAGE I                                1                               7
  STAGE IA                               2                               2
  STAGE IB                               3                               3
  STAGE II                               0                               1
  STAGE IIA                             14                              21
  STAGE IIB                              6                              20
  STAGE III                             13                              10
  STAGE IIIA                             3                               8
  STAGE IIIB                             1                               7
  STAGE IIIC                             3                               3
  STAGE IV                               1                               2
  STAGE IVA                              2                               0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  AMP PEAK 27(18P11.32) MUTATED       7 10 34  0
  AMP PEAK 27(18P11.32) WILD-TYPE    19 23 40  4
D27V4, multiclass
       clus
vv      AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  T0+T1                             7                              19
  T2                               10                              23
  T3                               34                              40
  T4                                0                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  AMP PEAK 27(18P11.32) MUTATED   23 21  3  3
  AMP PEAK 27(18P11.32) WILD-TYPE 41 33  8  3
D27V5, multiclass
    clus
vv   AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  N0                            23                              41
  N1                            21                              33
  N2                             3                               8
  N3                             3                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  AMP PEAK 27(18P11.32) MUTATED   39  0   3  8
  AMP PEAK 27(18P11.32) WILD-TYPE 72  2   0  9
D27V6, multiclass
     clus
vv    AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  M0                             39                              72
  M1                              0                               2
  M1A                             3                               0
  MX                              8                               9
[1] 4 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
  AMP PEAK 27(18P11.32) MUTATED    3 52
  AMP PEAK 27(18P11.32) WILD-TYPE 18 77
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(18P11.32) MUTATED      3   52
  AMP PEAK 27(18P11.32) WILD-TYPE   18   77
        clus
vv       AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  FEMALE                             3                              18
  MALE                              52                              77
[1] 2 2
[1] FALSE
D27V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(18P11.32) MUTATED      19                         1    27
  AMP PEAK 27(18P11.32) WILD-TYPE    19                         1    66
D27V9, multiclass
                           clus
vv                          AMP PEAK 27(18P11.32) MUTATED
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                27
                           clus
vv                          AMP PEAK 27(18P11.32) WILD-TYPE
  ASIAN                                                  19
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = AMP PEAK 28(18Q11.2) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 28(18Q11.2) MUTATED   30 17
  AMP PEAK 28(18Q11.2) WILD-TYPE 58 37
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            47                             95 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            17                             37 
$`AMP PEAK 28(18Q11.2) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A50L 
       58.55         7.63        13.94         4.21        33.27         0.53 
TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
        0.36        60.39        42.77         3.16         3.45         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW 
        3.52         3.35        18.35         3.32         3.16         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        2.60         0.36         3.02        55.50         2.66        13.48 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         5.42        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
       46.09        10.36         0.07         0.10         0.07         0.10 
TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
        0.10         1.18         3.78         7.59         5.06        29.59 
TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RE TCGA-VR-A8Q7 TCGA-VR-AA7I 
       53.95        14.01         4.80        36.72        15.91 

$`AMP PEAK 28(18Q11.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         5.92         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45        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-A5S3 
        0.03         0.26         0.99        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.13        14.86         0.46         0.43       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
       25.28        18.08        17.59         6.21         0.30         4.31 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP 
        3.68        19.50         8.78         6.41         4.08         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        1.38        30.74         4.90        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH 
        8.71        25.12         7.40         3.95        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-LN-A49L 
       16.47        13.55         7.76        21.37         8.71        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-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10         0.07         0.07         0.13         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.07         0.07         0.20        17.62         5.16 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        8.02        14.70         7.04         6.35         9.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        8.78         5.29         3.42         8.48         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
       18.31         8.12        12.03         9.17        18.12 

  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                         83.24                         122.10 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                          7.13                           7.76 
[1] "0.1 - 83.2 (7.1)"  "0.0 - 122.1 (7.8)"
[1] "hr=" "1.4"
D28V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(18Q11.2) MUTATED         5        1        3        0         7
  AMP PEAK 28(18Q11.2) WILD-TYPE       3        3        3        1        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(18Q11.2) MUTATED           7        10          2          3
  AMP PEAK 28(18Q11.2) WILD-TYPE        19        13          9          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 28(18Q11.2) MUTATED            2        0         1
  AMP PEAK 28(18Q11.2) WILD-TYPE          4        3         1
D28V3, multiclass
            clus
vv           AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              1                              3
  STAGE IB                              3                              3
  STAGE II                              0                              1
  STAGE IIA                             7                             28
  STAGE IIB                             7                             19
  STAGE III                            10                             13
  STAGE IIIA                            2                              9
  STAGE IIIB                            3                              5
  STAGE IIIC                            2                              4
  STAGE IV                              0                              3
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 28(18Q11.2) MUTATED      11  8 23  1
  AMP PEAK 28(18Q11.2) WILD-TYPE    15 25 51  3
D28V4, multiclass
       clus
vv      AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  T0+T1                           11                             15
  T2                               8                             25
  T3                              23                             51
  T4                               1                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 28(18Q11.2) MUTATED   20 17  4  2
  AMP PEAK 28(18Q11.2) WILD-TYPE 44 37  7  4
D28V5, multiclass
    clus
vv   AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  N0                           20                             44
  N1                           17                             37
  N2                            4                              7
  N3                            2                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 28(18Q11.2) MUTATED   34  0   1  6
  AMP PEAK 28(18Q11.2) WILD-TYPE 77  2   2 11
D28V6, multiclass
     clus
vv    AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  M0                            34                             77
  M1                             0                              2
  M1A                            1                              2
  MX                             6                             11
[1] 4 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
  AMP PEAK 28(18Q11.2) MUTATED    6 42
  AMP PEAK 28(18Q11.2) WILD-TYPE 15 87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(18Q11.2) MUTATED      6   42
  AMP PEAK 28(18Q11.2) WILD-TYPE   15   87
        clus
vv       AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  FEMALE                            6                             15
  MALE                             42                             87
[1] 2 2
[1] FALSE
D28V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(18Q11.2) MUTATED       9                         0    33
  AMP PEAK 28(18Q11.2) WILD-TYPE    29                         2    60
D28V9, multiclass
                           clus
vv                          AMP PEAK 28(18Q11.2) MUTATED
  ASIAN                                                9
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               33
                           clus
vv                          AMP PEAK 28(18Q11.2) WILD-TYPE
  ASIAN                                                 29
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = AMP PEAK 29(19P13.2) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 29(19P13.2) MUTATED   18  6
  AMP PEAK 29(19P13.2) WILD-TYPE 70 48
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                            24                            118 
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                             6                             48 
$`AMP PEAK 29(19P13.2) MUTATED`
TCGA-2H-A9GH TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A51D TCGA-L5-A43C TCGA-L5-A43J 
       31.27        20.09        20.12        17.03         3.16         4.31 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NF 
        3.16        29.00         2.60         0.36         3.95         2.66 
TCGA-L5-A8NK TCGA-L5-A8NT TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4A3 
       13.55        27.12         0.07         0.33         0.10         0.07 
TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-AA7I 
        0.10         1.18        14.01         8.48         8.15        15.91 

$`AMP PEAK 29(19P13.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 
        8.94        16.24         4.21        32.45        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63         0.03         0.26         0.99         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41         0.36         0.13        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.43       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       18.08        17.59         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-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.02        55.50        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        83.24        52.57        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        0.16         0.07         0.10         0.13         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.07         0.13         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.10         0.07         0.20        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-RE-A7BO TCGA-S8-A6BV 
       29.59         6.35        53.95         9.30         7.00         8.78 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        5.29         3.42         4.80         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
       36.72        12.03         9.17        18.12 

  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                         31.27                         122.10 
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                          4.13                           7.61 
[1] "0.1 - 31.3 (4.1)"  "0.0 - 122.1 (7.6)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(19P13.2) MUTATED         0        1        1        1         8
  AMP PEAK 29(19P13.2) WILD-TYPE       8        3        5        0        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(19P13.2) MUTATED           6         3          1          0
  AMP PEAK 29(19P13.2) WILD-TYPE        20        20         10          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 29(19P13.2) MUTATED            0        0         1
  AMP PEAK 29(19P13.2) WILD-TYPE          6        3         1
D29V3, multiclass
            clus
vv           AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  STAGE I                               0                              8
  STAGE IA                              1                              3
  STAGE IB                              1                              5
  STAGE II                              1                              0
  STAGE IIA                             8                             27
  STAGE IIB                             6                             20
  STAGE III                             3                             20
  STAGE IIIA                            1                             10
  STAGE IIIB                            0                              8
  STAGE IIIC                            0                              6
  STAGE IV                              0                              3
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 29(19P13.2) MUTATED       5  4 14  1
  AMP PEAK 29(19P13.2) WILD-TYPE    21 29 60  3
D29V4, multiclass
       clus
vv      AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  T0+T1                            5                             21
  T2                               4                             29
  T3                              14                             60
  T4                               1                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 29(19P13.2) MUTATED   18  6  0  0
  AMP PEAK 29(19P13.2) WILD-TYPE 46 48 11  6
D29V5, multiclass
    clus
vv   AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  N0                           18                             46
  N1                            6                             48
  N2                            0                             11
  N3                            0                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 29(19P13.2) MUTATED   17  0   1  6
  AMP PEAK 29(19P13.2) WILD-TYPE 94  2   2 11
D29V6, multiclass
     clus
vv    AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  M0                            17                             94
  M1                             0                              2
  M1A                            1                              2
  MX                             6                             11
[1] 4 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
  AMP PEAK 29(19P13.2) MUTATED     1  25
  AMP PEAK 29(19P13.2) WILD-TYPE  20 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(19P13.2) MUTATED      1   25
  AMP PEAK 29(19P13.2) WILD-TYPE   20  104
        clus
vv       AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  FEMALE                            1                             20
  MALE                             25                            104
[1] 2 2
[1] FALSE
D29V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(19P13.2) MUTATED       8                         1    16
  AMP PEAK 29(19P13.2) WILD-TYPE    30                         1    77
D29V9, multiclass
                           clus
vv                          AMP PEAK 29(19P13.2) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               16
                           clus
vv                          AMP PEAK 29(19P13.2) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = AMP PEAK 30(19Q12) MUTATION ANALYSIS
D30V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 30(19Q12) MUTATED   27 14
  AMP PEAK 30(19Q12) WILD-TYPE 61 40
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          41                          101 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          14                           40 
$`AMP PEAK 30(19Q12) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A3QL TCGA-IG-A4QS 
       31.27        58.55         7.63         8.94        20.09         0.26 
TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OF 
       23.41         0.43        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-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR 
        3.95        55.50        35.97        13.55         5.42         8.71 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       27.12        52.57        46.09        10.36         0.07        10.45 
TCGA-LN-A49U TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        0.07         0.10         0.10         5.06        14.70        29.59 
TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8Q7 TCGA-VR-AA7I 
       53.95        14.01         8.48        36.72        15.91 

$`AMP PEAK 30(19Q12) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        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-A6FA TCGA-JY-A6FB 
        0.13        14.86         0.46       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       25.28        18.08        17.59         6.21         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31         8.94         3.35         8.78         6.41         4.08 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         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-A893 
        8.71         2.60        25.12         0.36         7.40         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       21.37        13.41        83.24         0.16         0.07         0.33 
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-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.13         0.07         0.10         0.07         0.07         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-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        8.02         7.59         7.04         6.35         9.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        8.78         5.29         3.42         4.80         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
       18.31         8.12        12.03         9.17        18.12 

  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                       58.55                       122.10 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                       10.45                         7.00 
[1] "0.1 - 58.5 (10.4)" "0.0 - 122.1 (7.0)"
[1] "hr=" "1.7"
D30V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(19Q12) MUTATED         2        1        2        0         9
  AMP PEAK 30(19Q12) WILD-TYPE       6        3        4        1        26
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(19Q12) MUTATED          10         7          2          2
  AMP PEAK 30(19Q12) WILD-TYPE        16        16          9          6
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 30(19Q12) MUTATED            2        0         0
  AMP PEAK 30(19Q12) WILD-TYPE          4        3         2
D30V3, multiclass
            clus
vv           AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  STAGE I                             2                            6
  STAGE IA                            1                            3
  STAGE IB                            2                            4
  STAGE II                            0                            1
  STAGE IIA                           9                           26
  STAGE IIB                          10                           16
  STAGE III                           7                           16
  STAGE IIIA                          2                            9
  STAGE IIIB                          2                            6
  STAGE IIIC                          2                            4
  STAGE IV                            0                            3
  STAGE IVA                           0                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 30(19Q12) MUTATED       6  9 22  1
  AMP PEAK 30(19Q12) WILD-TYPE    20 24 52  3
D30V4, multiclass
       clus
vv      AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  T0+T1                          6                           20
  T2                             9                           24
  T3                            22                           52
  T4                             1                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 30(19Q12) MUTATED   17 15  3  2
  AMP PEAK 30(19Q12) WILD-TYPE 47 39  8  4
D30V5, multiclass
    clus
vv   AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  N0                         17                           47
  N1                         15                           39
  N2                          3                            8
  N3                          2                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 M1A MX
  AMP PEAK 30(19Q12) MUTATED   30  0   0  5
  AMP PEAK 30(19Q12) WILD-TYPE 81  2   3 12
D30V6, multiclass
     clus
vv    AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  M0                          30                           81
  M1                           0                            2
  M1A                          0                            3
  MX                           5                           12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                              cls
clus                            0  1
  AMP PEAK 30(19Q12) MUTATED    4 39
  AMP PEAK 30(19Q12) WILD-TYPE 17 90
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED      4   39
  AMP PEAK 30(19Q12) WILD-TYPE   17   90
        clus
vv       AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  FEMALE                          4                           17
  MALE                           39                           90
[1] 2 2
[1] FALSE
D30V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(19Q12) MUTATED       8                         1    29
  AMP PEAK 30(19Q12) WILD-TYPE    30                         1    64
D30V9, multiclass
                           clus
vv                          AMP PEAK 30(19Q12) MUTATED
  ASIAN                                              8
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             29
                           clus
vv                          AMP PEAK 30(19Q12) WILD-TYPE
  ASIAN                                               30
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = AMP PEAK 31(XQ28) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 31(XQ28) MUTATED   31 18
  AMP PEAK 31(XQ28) WILD-TYPE 57 36
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                         49                          93 
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                         18                          36 
$`AMP PEAK 31(XQ28) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS 
       14.30         5.92        16.24        20.09        20.78         0.26 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.53        17.03        23.41         0.36         0.13         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A43J 
      122.10        44.75        25.41        23.18         3.45         4.31 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A8NK 
        3.52         8.78         4.08        18.35         1.38        13.55 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.10         0.10         0.13         0.10         0.10 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-S8-A6BV TCGA-V5-A7RB 
        0.07         1.18         8.02        14.70         8.78         5.29 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I 
        8.48         4.44        18.31         8.12        36.72        15.91 
TCGA-ZR-A9CJ 
       18.12 

$`AMP PEAK 31(XQ28) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
        4.21        32.45        33.27         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6FB 
        0.03         0.99         0.79        14.86         0.43        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        42.77        15.48        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M 
       18.08        17.59         6.21         3.16         0.30         8.94 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
        3.68         3.35        19.50         6.41         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.74         4.90        29.00         7.13         7.43 
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-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       13.48        16.47        13.22         7.76         5.42         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49O 
       13.41        27.12        83.24        52.57        46.09         0.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.13         0.07         0.07         0.07         0.07         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.07         0.10         0.20        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        3.78         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
       53.95         9.30         7.00        14.01         3.42         4.80 
TCGA-V5-AASW TCGA-VR-AA4G TCGA-VR-AA7D 
        8.15        12.03         9.17 

  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                       0.07                        0.03 
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                     122.10                       83.24 
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                       8.02                        7.43 
[1] "0.1 - 122.1 (8.0)" "0.0 - 83.2 (7.4)" 
[1] "hr=" "1.1"
D31V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 31(XQ28) MUTATED         2        1        0        0        15
  AMP PEAK 31(XQ28) WILD-TYPE       6        3        6        1        20
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 31(XQ28) MUTATED          10         5          5          6
  AMP PEAK 31(XQ28) WILD-TYPE        16        18          6          2
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 31(XQ28) MUTATED            3        1         1
  AMP PEAK 31(XQ28) WILD-TYPE          3        2         1
D31V3, multiclass
            clus
vv           AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  STAGE I                            2                           6
  STAGE IA                           1                           3
  STAGE IB                           0                           6
  STAGE II                           0                           1
  STAGE IIA                         15                          20
  STAGE IIB                         10                          16
  STAGE III                          5                          18
  STAGE IIIA                         5                           6
  STAGE IIIB                         6                           2
  STAGE IIIC                         3                           3
  STAGE IV                           1                           2
  STAGE IVA                          1                           1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK 31(XQ28) MUTATED       7 12 29  2
  AMP PEAK 31(XQ28) WILD-TYPE    19 21 45  2
D31V4, multiclass
       clus
vv      AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  T0+T1                         7                          19
  T2                           12                          21
  T3                           29                          45
  T4                            2                           2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  AMP PEAK 31(XQ28) MUTATED   25 15  7  3
  AMP PEAK 31(XQ28) WILD-TYPE 39 39  4  3
D31V5, multiclass
    clus
vv   AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  N0                        25                          39
  N1                        15                          39
  N2                         7                           4
  N3                         3                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 M1A MX
  AMP PEAK 31(XQ28) MUTATED   37  1   1  8
  AMP PEAK 31(XQ28) WILD-TYPE 74  1   2  9
D31V6, multiclass
     clus
vv    AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  M0                         37                          74
  M1                          1                           1
  M1A                         1                           2
  MX                          8                           9
[1] 4 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
  AMP PEAK 31(XQ28) MUTATED    3 50
  AMP PEAK 31(XQ28) WILD-TYPE 18 79
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 31(XQ28) MUTATED      3   50
  AMP PEAK 31(XQ28) WILD-TYPE   18   79
        clus
vv       AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  FEMALE                         3                          18
  MALE                          50                          79
[1] 2 2
[1] FALSE
D31V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(XQ28) MUTATED      22                         1    26
  AMP PEAK 31(XQ28) WILD-TYPE    16                         1    67
D31V9, multiclass
                           clus
vv                          AMP PEAK 31(XQ28) MUTATED
  ASIAN                                            22
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            26
                           clus
vv                          AMP PEAK 31(XQ28) WILD-TYPE
  ASIAN                                              16
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.11) MUTATED   33 24
  DEL PEAK  1(1P36.11) WILD-TYPE 55 30
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            57                             85 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            24                             30 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A4P3 TCGA-IG-A4QS 
       16.24        32.45        33.27        20.09         0.03         0.26 
TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C 
        0.53         0.36       122.10        60.39        42.77        23.18 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94         3.52         3.68         3.35 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.74         4.90        29.00         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG 
        2.60         0.36         7.40         3.02        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-LN-A49K 
       12.92        16.47        13.22         5.42        13.41         0.07 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.10         0.07         0.20         1.18         8.02         7.59 
TCGA-R6-A6KZ TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        5.06        14.01         3.42         4.80         8.15         4.44 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
        8.12        36.72        18.12 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       25.78         5.92         4.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12         0.99        17.03         0.79        23.41         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         0.46         0.43        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        25.41        15.48        25.28        18.08        17.59 
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-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A88S 
        4.08        18.35         3.32         7.17         1.38         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK 
        8.71        25.12         3.95         2.66        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36        10.45         0.16         0.07         0.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.13         0.07         0.10         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-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 
        0.10         0.07        17.62         5.16         3.78        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-AASV TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7D 
        8.78         5.29         8.48        18.31        12.03         9.17 
TCGA-VR-AA7I 
       15.91 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          7.63                           7.04 
[1] "0.0 - 122.1 (7.6)" "0.1 - 83.2 (7.0)" 
[1] "hr=" "1"  
D32V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         5        1        2        0         8
  DEL PEAK  1(1P36.11) WILD-TYPE       3        3        4        1        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          13        12          2          5
  DEL PEAK  1(1P36.11) WILD-TYPE        13        11          9          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  1(1P36.11) MUTATED            1        2         1
  DEL PEAK  1(1P36.11) WILD-TYPE          5        1         1
D32V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              1                              3
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                             8                             27
  STAGE IIB                            13                             13
  STAGE III                            12                             11
  STAGE IIIA                            2                              9
  STAGE IIIB                            5                              3
  STAGE IIIC                            1                              5
  STAGE IV                              2                              1
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK  1(1P36.11) MUTATED      13 11 30  0
  DEL PEAK  1(1P36.11) WILD-TYPE    13 22 44  4
D32V4, multiclass
       clus
vv      DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1                           13                             13
  T2                              11                             22
  T3                              30                             44
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK  1(1P36.11) MUTATED   20 27  6  1
  DEL PEAK  1(1P36.11) WILD-TYPE 44 27  5  5
D32V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           20                             44
  N1                           27                             27
  N2                            6                              5
  N3                            1                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK  1(1P36.11) MUTATED   42  1   2  7
  DEL PEAK  1(1P36.11) WILD-TYPE 69  1   1 10
D32V6, multiclass
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                            42                             69
  M1                             1                              1
  M1A                            2                              1
  MX                             7                             10
[1] 4 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  1(1P36.11) MUTATED    8 52
  DEL PEAK  1(1P36.11) WILD-TYPE 13 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      8   52
  DEL PEAK  1(1P36.11) WILD-TYPE   13   77
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                            8                             13
  MALE                             52                             77
[1] 2 2
[1] FALSE
D32V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED      12                         1    37
  DEL PEAK  1(1P36.11) WILD-TYPE    26                         1    56
D32V9, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               37
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                 26
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P13.2) MUTATED   28 20
  DEL PEAK  2(1P13.2) WILD-TYPE 60 34
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           48                            94 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           20                            34 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       14.30         7.63        13.94         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.09         2.63         0.03         0.26         0.53         0.79 
TCGA-IG-A8O2 TCGA-JY-A6FE TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
        0.46         3.68         0.30         8.94         3.52         3.35 
TCGA-L5-A4OH TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       19.50         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         0.36         7.40        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49W 
       12.92        13.48        16.47        13.41         0.07         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-R6-A6DQ 
        0.10         0.07         0.20         1.18        17.62         7.59 
TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW 
       53.95        14.01         3.42         8.15         4.44         8.12 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         5.92         8.94        16.24 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
        0.85        20.78        20.12         0.99        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.36         0.13        14.86         0.43       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02        41.52        42.77        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.45         4.31         3.68         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-A88T TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NL 
        8.71        25.12         3.95         3.02        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.42        21.37         8.71        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.36        10.45         0.16         0.07 
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-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.07         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.10         0.07         5.16         3.78         8.02         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 TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8Q7 
        8.78         5.29         4.80         8.48        18.31        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       12.03         9.17        15.91        18.12 

  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 
                         55.5                         122.1 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        7.035                         8.595 
[1] "0.0 - 55.5 (7.0)"  "0.1 - 122.1 (8.6)"
[1] "hr=" "1.5"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED         2        0        3        0        12
  DEL PEAK  2(1P13.2) WILD-TYPE       6        4        3        1        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED           8        11          2          4
  DEL PEAK  2(1P13.2) WILD-TYPE        18        12          9          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  2(1P13.2) MUTATED            0        2         1
  DEL PEAK  2(1P13.2) WILD-TYPE          6        1         1
D33V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             4
  STAGE IB                             3                             3
  STAGE II                             0                             1
  STAGE IIA                           12                            23
  STAGE IIB                            8                            18
  STAGE III                           11                            12
  STAGE IIIA                           2                             9
  STAGE IIIB                           4                             4
  STAGE IIIC                           0                             6
  STAGE IV                             2                             1
  STAGE IVA                            1                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  2(1P13.2) MUTATED       7 11 29  0
  DEL PEAK  2(1P13.2) WILD-TYPE    19 22 45  4
D33V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T0+T1                           7                            19
  T2                             11                            22
  T3                             29                            45
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  2(1P13.2) MUTATED   21 21  5  0
  DEL PEAK  2(1P13.2) WILD-TYPE 43 33  6  6
D33V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          21                            43
  N1                          21                            33
  N2                           5                             6
  N3                           0                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  2(1P13.2) MUTATED   38  1   2  5
  DEL PEAK  2(1P13.2) WILD-TYPE 73  1   1 12
D33V6, multiclass
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  M0                           38                            73
  M1                            1                             1
  M1A                           2                             1
  MX                            5                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    6 46
  DEL PEAK  2(1P13.2) WILD-TYPE 15 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6   46
  DEL PEAK  2(1P13.2) WILD-TYPE   15   83
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                           6                            15
  MALE                            46                            83
[1] 2 2
[1] FALSE
D33V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.2) MUTATED      13                         1    30
  DEL PEAK  2(1P13.2) WILD-TYPE    25                         1    63
D33V9, multiclass
                           clus
vv                          DEL PEAK  2(1P13.2) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              30
                           clus
vv                          DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                                                25
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D34V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(1Q44) MUTATED    9  6
  DEL PEAK  3(1Q44) WILD-TYPE 79 48
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         15                         127 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          6                          48 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-IG-A4QS TCGA-IG-A6QS TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A8NG 
        0.26         0.13         3.52         6.41         3.32        35.97 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4A5 
       83.24        10.36         0.07         0.33         0.07         0.10 
TCGA-R6-A6DQ TCGA-R6-A6Y0 TCGA-VR-AA7D 
        7.59        53.95         9.17 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12         0.03 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        0.99         0.53        17.03         0.79        23.41         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         0.46         0.43       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        3.45         0.30         4.31         8.94         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.50         8.78         4.08        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.74         4.90        29.00         7.13         7.43 
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-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L 
        8.71        13.41        27.12        52.57        46.09        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-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.07         0.10         0.13         0.07         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-A6KZ TCGA-R6-A6L4 
       17.62         5.16         3.78         8.02         5.06        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 TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       14.01         5.29         3.42         4.80         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I 
        4.44        18.31         8.12        36.72        12.03        15.91 
TCGA-ZR-A9CJ 
       18.12 

  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 
                       3.52                        7.76 
[1] "0.1 - 83.2 (3.5)"  "0.0 - 122.1 (7.8)"
[1] "hr=" "1.1"
D34V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(1Q44) MUTATED         1        0        0        0         6
  DEL PEAK  3(1Q44) WILD-TYPE       7        4        6        1        29
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q44) MUTATED           1         1          0          2
  DEL PEAK  3(1Q44) WILD-TYPE        25        22         11          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  3(1Q44) MUTATED            3        0         0
  DEL PEAK  3(1Q44) WILD-TYPE          3        3         2
D34V3, multiclass
            clus
vv           DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                            1                           7
  STAGE IA                           0                           4
  STAGE IB                           0                           6
  STAGE II                           0                           1
  STAGE IIA                          6                          29
  STAGE IIB                          1                          25
  STAGE III                          1                          22
  STAGE IIIA                         0                          11
  STAGE IIIB                         2                           6
  STAGE IIIC                         3                           3
  STAGE IV                           0                           3
  STAGE IVA                          0                           2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK  3(1Q44) MUTATED       1  4  9  0
  DEL PEAK  3(1Q44) WILD-TYPE    25 29 65  4
D34V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T0+T1                         1                          25
  T2                            4                          29
  T3                            9                          65
  T4                            0                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK  3(1Q44) MUTATED    7  2  2  3
  DEL PEAK  3(1Q44) WILD-TYPE 57 52  9  3
D34V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                         7                          57
  N1                         2                          52
  N2                         2                           9
  N3                         3                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 M1A MX
  DEL PEAK  3(1Q44) MUTATED   12  0   0  1
  DEL PEAK  3(1Q44) WILD-TYPE 99  2   3 16
D34V6, multiclass
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  M0                         12                          99
  M1                          0                           2
  M1A                         0                           3
  MX                          1                          16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     2  14
  DEL PEAK  3(1Q44) WILD-TYPE  19 115
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      2   14
  DEL PEAK  3(1Q44) WILD-TYPE   19  115
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                         2                          19
  MALE                          14                         115
[1] 2 2
[1] FALSE
D34V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q44) MUTATED       5                         0    10
  DEL PEAK  3(1Q44) WILD-TYPE    33                         2    83
D34V9, multiclass
                           clus
vv                          DEL PEAK  3(1Q44) MUTATED
  ASIAN                                             5
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            10
                           clus
vv                          DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                                              33
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q22.1) MUTATED   21 17
  DEL PEAK  4(2Q22.1) WILD-TYPE 67 37
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           38                           104 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           17                            37 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       58.55         4.21        33.27         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.03         0.53        17.03         0.79         0.13         0.46 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OE 
       44.75        68.02        41.52         3.16         0.30         3.52 
TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NV 
       30.74         7.43         7.40         3.02        13.55        52.57 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-Q9-A6FU 
       10.36        10.45         0.07         0.10         0.20         5.16 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RB TCGA-VR-A8EU TCGA-VR-A8EW 
       29.59        53.95        14.01         5.29        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA7I 
       36.72        15.91 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS 
        8.94        16.24        32.45        20.09        20.78         0.26 
TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 
        0.99        23.41         0.36        14.86         0.43       122.10 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       60.39         3.68        42.77        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J 
       25.28        18.08        17.59         6.21         3.45         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94         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-A4OR 
        4.08        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
       25.12         0.36         3.95        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
       21.37         8.71        13.41        27.12        83.24        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        0.07         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V 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-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 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-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        1.18        17.62         3.78         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
       14.70         7.04         6.35         9.30         7.00         8.78 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4G 
        3.42         4.80         8.48         8.15         4.44        12.03 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

  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 
                        68.02                        122.10 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        7.775                         7.380 
[1] "0.0 - 68.0 (7.8)"  "0.1 - 122.1 (7.4)"
[1] "hr=" "1"  
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(2Q22.1) MUTATED         2        0        2        0        12
  DEL PEAK  4(2Q22.1) WILD-TYPE       6        4        4        1        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2Q22.1) MUTATED           7         5          5          4
  DEL PEAK  4(2Q22.1) WILD-TYPE        19        18          6          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  4(2Q22.1) MUTATED            1        1         0
  DEL PEAK  4(2Q22.1) WILD-TYPE          5        2         2
D35V3, multiclass
            clus
vv           DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             4
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                           12                            23
  STAGE IIB                            7                            19
  STAGE III                            5                            18
  STAGE IIIA                           5                             6
  STAGE IIIB                           4                             4
  STAGE IIIC                           1                             5
  STAGE IV                             1                             2
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  4(2Q22.1) MUTATED       6 13 19  2
  DEL PEAK  4(2Q22.1) WILD-TYPE    20 20 55  2
D35V4, multiclass
       clus
vv      DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T0+T1                           6                            20
  T2                             13                            20
  T3                             19                            55
  T4                              2                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  4(2Q22.1) MUTATED   17 18  4  1
  DEL PEAK  4(2Q22.1) WILD-TYPE 47 36  7  5
D35V5, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                          17                            47
  N1                          18                            36
  N2                           4                             7
  N3                           1                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  4(2Q22.1) MUTATED   35  1   0  3
  DEL PEAK  4(2Q22.1) WILD-TYPE 76  1   3 14
D35V6, multiclass
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  M0                           35                            76
  M1                            1                             1
  M1A                           0                             3
  MX                            3                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED    7 36
  DEL PEAK  4(2Q22.1) WILD-TYPE 14 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      7   36
  DEL PEAK  4(2Q22.1) WILD-TYPE   14   93
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                           7                            14
  MALE                            36                            93
[1] 2 2
[1] FALSE
D35V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q22.1) MUTATED      13                         0    27
  DEL PEAK  4(2Q22.1) WILD-TYPE    25                         2    66
D35V9, multiclass
                           clus
vv                          DEL PEAK  4(2Q22.1) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              27
                           clus
vv                          DEL PEAK  4(2Q22.1) WILD-TYPE
  ASIAN                                                25
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK  5(2Q33.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q33.3) MUTATED   16  6
  DEL PEAK  5(2Q33.3) WILD-TYPE 72 48
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           22                           120 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                            6                            48 
$`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-JY-A93E TCGA-L5-A43H TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A893 
       68.02        18.08         0.30        30.74         6.94         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-LN-A49K TCGA-LN-A49V TCGA-LN-A4MQ 
       16.47        13.55         5.42         0.07         0.10         0.10 
TCGA-R6-A6DN TCGA-S8-A6BV TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
        8.02         8.78        36.72        18.12 

$`DEL PEAK  5(2Q33.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.78         0.26         0.99         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.36         0.13        14.86         0.46         0.43       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       44.75        60.39         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        23.18        25.28        17.59         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-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        46.09        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-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       14.01         5.29         3.42         4.80         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        4.44        18.31         8.12        12.03         9.17        15.91 

  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 
                        68.02                        122.10 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                         7.48                          7.51 
[1] "0.0 - 68.0 (7.5)"  "0.1 - 122.1 (7.5)"
[1] "hr=" "1.3"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q33.3) MUTATED         1        0        2        0         7
  DEL PEAK  5(2Q33.3) WILD-TYPE       7        4        4        1        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q33.3) MUTATED           3         4          6          0
  DEL PEAK  5(2Q33.3) WILD-TYPE        23        19          5          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  5(2Q33.3) MUTATED            1        0         0
  DEL PEAK  5(2Q33.3) WILD-TYPE          5        3         2
D36V3, multiclass
            clus
vv           DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             0                             4
  STAGE IB                             2                             4
  STAGE II                             0                             1
  STAGE IIA                            7                            28
  STAGE IIB                            3                            23
  STAGE III                            4                            19
  STAGE IIIA                           6                             5
  STAGE IIIB                           0                             8
  STAGE IIIC                           1                             5
  STAGE IV                             0                             3
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  5(2Q33.3) MUTATED       1  5 17  1
  DEL PEAK  5(2Q33.3) WILD-TYPE    25 28 57  3
D36V4, multiclass
       clus
vv      DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  T0+T1                           1                            25
  T2                              5                            28
  T3                             17                            57
  T4                              1                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  5(2Q33.3) MUTATED   12 11  0  1
  DEL PEAK  5(2Q33.3) WILD-TYPE 52 43 11  5
D36V5, multiclass
    clus
vv   DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  N0                          12                            52
  N1                          11                            43
  N2                           0                            11
  N3                           1                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  5(2Q33.3) MUTATED   21  0   0  3
  DEL PEAK  5(2Q33.3) WILD-TYPE 90  2   3 14
D36V6, multiclass
     clus
vv    DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  M0                           21                            90
  M1                            0                             2
  M1A                           0                             3
  MX                            3                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q33.3) MUTATED     4  21
  DEL PEAK  5(2Q33.3) WILD-TYPE  17 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED      4   21
  DEL PEAK  5(2Q33.3) WILD-TYPE   17  108
        clus
vv       DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  FEMALE                           4                            17
  MALE                            21                           108
[1] 2 2
[1] FALSE
D36V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q33.3) MUTATED       7                         0    18
  DEL PEAK  5(2Q33.3) WILD-TYPE    31                         2    75
D36V9, multiclass
                           clus
vv                          DEL PEAK  5(2Q33.3) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              18
                           clus
vv                          DEL PEAK  5(2Q33.3) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK  6(3P26.2) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(3P26.2) MUTATED   52 27
  DEL PEAK  6(3P26.2) WILD-TYPE 36 27
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                           79                            63 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                           27                            27 
$`DEL PEAK  6(3P26.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         5.92        13.94         8.94        16.24         4.21 
TCGA-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-A5S3 TCGA-IG-A6QS 
        0.26         0.53        17.03         0.79        23.41         0.13 
TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
        0.43        60.39        68.02         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        8.94         3.35        19.50         4.08         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
        3.16        30.74         4.90         7.13         6.94         2.60 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        7.40        55.50         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       13.55         5.42        52.57         0.07         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.10         0.13         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-A4MQ 
        0.07         0.10         0.10         0.10         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.07         0.20         1.18        17.62         3.78         7.59 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC 
        7.04        29.59         7.00         8.78        14.01         3.42 
TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        8.15        18.31         8.12        36.72        12.03         9.17 
TCGA-VR-AA7I 
       15.91 

$`DEL PEAK  6(3P26.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GR TCGA-IG-A4P3 
       25.78        31.27        58.55         7.63        32.45         0.03 
TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.99         0.36        14.86         0.46       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OE 
       25.28        18.08        17.59         6.21         3.16         3.52 
TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU 
        3.68         8.78         6.41        18.35         1.38        29.00 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        7.43         8.71        25.12         0.36         3.95         3.02 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       27.12        83.24        46.09        10.36        10.45         0.16 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A9 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.10         0.07         0.07         5.16         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 
TCGA-V5-AASV TCGA-V5-AASX TCGA-ZR-A9CJ 
        8.48         4.44        18.12 

  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                         5.92                          8.78 
[1] "0.1 - 68.0 (5.9)"  "0.0 - 122.1 (8.8)"
[1] "hr=" "1.2"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(3P26.2) MUTATED         4        3        3        1        24
  DEL PEAK  6(3P26.2) WILD-TYPE       4        1        3        0        11
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P26.2) MUTATED          12        14          8          3
  DEL PEAK  6(3P26.2) WILD-TYPE        14         9          3          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  6(3P26.2) MUTATED            2        3         2
  DEL PEAK  6(3P26.2) WILD-TYPE          4        0         0
D37V3, multiclass
            clus
vv           DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             3                             1
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                           24                            11
  STAGE IIB                           12                            14
  STAGE III                           14                             9
  STAGE IIIA                           8                             3
  STAGE IIIB                           3                             5
  STAGE IIIC                           2                             4
  STAGE IV                             3                             0
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  6(3P26.2) MUTATED      14 18 45  3
  DEL PEAK  6(3P26.2) WILD-TYPE    12 15 29  1
D37V4, multiclass
       clus
vv      DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  T0+T1                          14                            12
  T2                             18                            15
  T3                             45                            29
  T4                              3                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  6(3P26.2) MUTATED   41 31  5  2
  DEL PEAK  6(3P26.2) WILD-TYPE 23 23  6  4
D37V5, multiclass
    clus
vv   DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  N0                          41                            23
  N1                          31                            23
  N2                           5                             6
  N3                           2                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  6(3P26.2) MUTATED   66  2   3  8
  DEL PEAK  6(3P26.2) WILD-TYPE 45  0   0  9
D37V6, multiclass
     clus
vv    DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  M0                           66                            45
  M1                            2                             0
  M1A                           3                             0
  MX                            8                             9
[1] 4 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  6(3P26.2) MUTATED   14 71
  DEL PEAK  6(3P26.2) WILD-TYPE  7 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED     14   71
  DEL PEAK  6(3P26.2) WILD-TYPE    7   58
        clus
vv       DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  FEMALE                          14                             7
  MALE                            71                            58
[1] 2 2
[1] FALSE
D37V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P26.2) MUTATED      27                         1    47
  DEL PEAK  6(3P26.2) WILD-TYPE    11                         1    46
D37V9, multiclass
                           clus
vv                          DEL PEAK  6(3P26.2) MUTATED
  ASIAN                                              27
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              47
                           clus
vv                          DEL PEAK  6(3P26.2) WILD-TYPE
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = DEL PEAK  7(3P14.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(3P14.3) MUTATED   57 33
  DEL PEAK  7(3P14.3) WILD-TYPE 31 21
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           90                            52 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           33                            21 
$`DEL PEAK  7(3P14.3) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         0.03         0.26         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       23.41         0.13         0.43        44.75        60.39        68.02 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        3.45         0.30         4.31         8.94         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.50         6.41         4.08         3.32         7.17         1.38 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         7.43         6.94         2.60         0.36         7.40 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN 
        2.66        35.97        12.92        16.47        13.55         5.42 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L 
        8.71        13.41        83.24        52.57         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-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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.10         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG 
        1.18        17.62         5.16         7.59         7.04        29.59 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EU 
        7.00         8.78        14.01         3.42         8.15        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.12        36.72        12.03         9.17        15.91        18.12 

$`DEL PEAK  7(3P14.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IG-A4QT TCGA-IG-A625 
       25.78        31.27        58.55         7.63         0.99         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       14.86         0.46       122.10         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OR 
        6.21         3.16         3.52         8.78        18.35         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 
       30.74         4.90        29.00         8.71        25.12         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        55.50        13.48        13.22         7.76        21.37 
TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49V TCGA-LN-A4A9 TCGA-Q9-A6FW 
       27.12        46.09        10.36         0.10         0.07         3.78 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         5.06        14.70         6.35        53.95         9.30 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        5.29         4.80         8.48         4.44 

  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 
                        6.675                         9.830 
[1] "0.0 - 83.2 (6.7)"  "0.1 - 122.1 (9.8)"
[1] "hr=" "1.4"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3P14.3) MUTATED         5        2        3        1        29
  DEL PEAK  7(3P14.3) WILD-TYPE       3        2        3        0         6
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P14.3) MUTATED          15        17          9          3
  DEL PEAK  7(3P14.3) WILD-TYPE        11         6          2          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  7(3P14.3) MUTATED            3        2         2
  DEL PEAK  7(3P14.3) WILD-TYPE          3        1         0
D38V3, multiclass
            clus
vv           DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             2
  STAGE IB                             3                             3
  STAGE II                             1                             0
  STAGE IIA                           29                             6
  STAGE IIB                           15                            11
  STAGE III                           17                             6
  STAGE IIIA                           9                             2
  STAGE IIIB                           3                             5
  STAGE IIIC                           3                             3
  STAGE IV                             2                             1
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  7(3P14.3) MUTATED      16 23 51  3
  DEL PEAK  7(3P14.3) WILD-TYPE    10 10 23  1
D38V4, multiclass
       clus
vv      DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  T0+T1                          16                            10
  T2                             23                            10
  T3                             51                            23
  T4                              3                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  7(3P14.3) MUTATED   48 35  6  3
  DEL PEAK  7(3P14.3) WILD-TYPE 16 19  5  3
D38V5, multiclass
    clus
vv   DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  N0                          48                            16
  N1                          35                            19
  N2                           6                             5
  N3                           3                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  7(3P14.3) MUTATED   77  2   2 10
  DEL PEAK  7(3P14.3) WILD-TYPE 34  0   1  7
D38V6, multiclass
     clus
vv    DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  M0                           77                            34
  M1                            2                             0
  M1A                           2                             1
  MX                           10                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED   16 82
  DEL PEAK  7(3P14.3) WILD-TYPE  5 47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED     16   82
  DEL PEAK  7(3P14.3) WILD-TYPE    5   47
        clus
vv       DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  FEMALE                          16                             5
  MALE                            82                            47
[1] 2 2
[1] FALSE
D38V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P14.3) MUTATED      33                         1    52
  DEL PEAK  7(3P14.3) WILD-TYPE     5                         1    41
D38V9, multiclass
                           clus
vv                          DEL PEAK  7(3P14.3) MUTATED
  ASIAN                                              33
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              52
                           clus
vv                          DEL PEAK  7(3P14.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"

Clustering(39) Variable = DEL PEAK  8(3P14.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(3P14.2) MUTATED   55 33
  DEL PEAK  8(3P14.2) WILD-TYPE 33 21
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           88                            54 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           33                            21 
$`DEL PEAK  8(3P14.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         0.03         0.26         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-L5-A43E 
       23.41         0.13         0.43        44.75        68.02         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.50         6.41         4.08         3.32         7.17         1.38 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         7.43         6.94         2.60         0.36         7.40 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN 
        2.66        35.97        12.92        16.47        13.55         5.42 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
        8.71        13.41        52.57         0.07        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
        0.07         0.33         0.13         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-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.10         0.07         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-S8-A6BV 
        5.16         8.02         7.59         7.04         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW 
       14.01         3.42         4.80         8.15        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       36.72        12.03         9.17        15.91 

$`DEL PEAK  8(3P14.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IG-A4QT TCGA-IG-A625 
       25.78        31.27        58.55         7.63         0.99         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         0.46       122.10        60.39         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        15.48        23.18        25.28        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OR 
       17.59         6.21         3.16         8.78        18.35         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 
       30.74         4.90        29.00         8.71        25.12         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        55.50        13.48        13.22         7.76        21.37 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49R TCGA-LN-A49V 
       27.12        83.24        46.09        10.36         0.10         0.10 
TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
        0.07         3.78         5.06        14.70        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-ZR-A9CJ 
       53.95         9.30         5.29         8.48         4.44        18.12 

  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 
                        68.02                        122.10 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         5.67                         14.09 
[1] "0.0 - 68.0 (5.7)"   "0.1 - 122.1 (14.1)"
[1] "hr=" "1.9"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P14.2) MUTATED         4        2        4        1        28
  DEL PEAK  8(3P14.2) WILD-TYPE       4        2        2        0         7
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P14.2) MUTATED          15        16          9          4
  DEL PEAK  8(3P14.2) WILD-TYPE        11         7          2          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  8(3P14.2) MUTATED            2        2         2
  DEL PEAK  8(3P14.2) WILD-TYPE          4        1         0
D39V3, multiclass
            clus
vv           DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             2                             2
  STAGE IB                             4                             2
  STAGE II                             1                             0
  STAGE IIA                           28                             7
  STAGE IIB                           15                            11
  STAGE III                           16                             7
  STAGE IIIA                           9                             2
  STAGE IIIB                           4                             4
  STAGE IIIC                           2                             4
  STAGE IV                             2                             1
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  8(3P14.2) MUTATED      16 22 50  3
  DEL PEAK  8(3P14.2) WILD-TYPE    10 11 24  1
D39V4, multiclass
       clus
vv      DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T0+T1                          16                            10
  T2                             22                            11
  T3                             50                            24
  T4                              3                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  8(3P14.2) MUTATED   47 34  7  2
  DEL PEAK  8(3P14.2) WILD-TYPE 17 20  4  4
D39V5, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                          47                            17
  N1                          34                            20
  N2                           7                             4
  N3                           2                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  8(3P14.2) MUTATED   75  2   2  9
  DEL PEAK  8(3P14.2) WILD-TYPE 36  0   1  8
D39V6, multiclass
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  M0                           75                            36
  M1                            2                             0
  M1A                           2                             1
  MX                            9                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED   16 80
  DEL PEAK  8(3P14.2) WILD-TYPE  5 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     16   80
  DEL PEAK  8(3P14.2) WILD-TYPE    5   49
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                          16                             5
  MALE                            80                            49
[1] 2 2
[1] FALSE
D39V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P14.2) MUTATED      32                         1    51
  DEL PEAK  8(3P14.2) WILD-TYPE     6                         1    42
D39V9, multiclass
                           clus
vv                          DEL PEAK  8(3P14.2) MUTATED
  ASIAN                                              32
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              51
                           clus
vv                          DEL PEAK  8(3P14.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"

Clustering(40) Variable = DEL PEAK  9(3Q11.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(3Q11.1) MUTATED   14  9
  DEL PEAK  9(3Q11.1) WILD-TYPE 74 45
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           23                           119 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                            9                            45 
$`DEL PEAK  9(3Q11.1) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YB TCGA-IG-A3YC 
       14.30        13.94         4.21        32.45         2.63        20.12 
TCGA-IG-A5S3 TCGA-JY-A6FD TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH 
       23.41        68.02        25.41         3.45         0.30        19.50 
TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A8NH TCGA-LN-A49L TCGA-LN-A49R 
        3.32         7.43         0.36        12.92        10.45         0.10 
TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-RE-A7BO TCGA-V5-AASW 
        0.07         0.10         0.20         7.00         8.15 

$`DEL PEAK  9(3Q11.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
       16.24        33.27        20.09         0.85        20.78         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.13        14.86         0.46         0.43       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       60.39         3.68        41.52        42.77        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43J 
       25.28        18.08        17.59         6.21         3.16         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-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        4.08        18.35         7.17         1.38         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        5.42        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.36         0.07         0.16         0.07 
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-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 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-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.07         1.18        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-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        6.35        53.95         9.30         8.78        14.01         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        3.42         4.80         8.48         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        12.03         9.17        15.91        18.12 

  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 
                        68.02                        122.10 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                         7.43                          7.59 
[1] "0.1 - 68.0 (7.4)"  "0.0 - 122.1 (7.6)"
[1] "hr=" "1.1"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3Q11.1) MUTATED         2        0        0        1         6
  DEL PEAK  9(3Q11.1) WILD-TYPE       6        4        6        0        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3Q11.1) MUTATED           6         5          2          0
  DEL PEAK  9(3Q11.1) WILD-TYPE        20        18          9          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  9(3Q11.1) MUTATED            1        1         0
  DEL PEAK  9(3Q11.1) WILD-TYPE          5        2         2
D40V3, multiclass
            clus
vv           DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             4
  STAGE IB                             0                             6
  STAGE II                             1                             0
  STAGE IIA                            6                            29
  STAGE IIB                            6                            20
  STAGE III                            5                            18
  STAGE IIIA                           2                             9
  STAGE IIIB                           0                             8
  STAGE IIIC                           1                             5
  STAGE IV                             1                             2
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  9(3Q11.1) MUTATED       6  6 13  0
  DEL PEAK  9(3Q11.1) WILD-TYPE    20 27 61  4
D40V4, multiclass
       clus
vv      DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  T0+T1                           6                            20
  T2                              6                            27
  T3                             13                            61
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  9(3Q11.1) MUTATED   13 11  0  1
  DEL PEAK  9(3Q11.1) WILD-TYPE 51 43 11  5
D40V5, multiclass
    clus
vv   DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  N0                          13                            51
  N1                          11                            43
  N2                           0                            11
  N3                           1                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  9(3Q11.1) MUTATED   23  1   0  1
  DEL PEAK  9(3Q11.1) WILD-TYPE 88  1   3 16
D40V6, multiclass
     clus
vv    DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  M0                           23                            88
  M1                            1                             1
  M1A                           0                             3
  MX                            1                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.1) MUTATED     3  23
  DEL PEAK  9(3Q11.1) WILD-TYPE  18 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED      3   23
  DEL PEAK  9(3Q11.1) WILD-TYPE   18  106
        clus
vv       DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  FEMALE                           3                            18
  MALE                            23                           106
[1] 2 2
[1] FALSE
D40V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3Q11.1) MUTATED       9                         0    13
  DEL PEAK  9(3Q11.1) WILD-TYPE    29                         2    80
D40V9, multiclass
                           clus
vv                          DEL PEAK  9(3Q11.1) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              13
                           clus
vv                          DEL PEAK  9(3Q11.1) WILD-TYPE
  ASIAN                                                29
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK 10(3Q26.31) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(3Q26.31) MUTATED    4  9
  DEL PEAK 10(3Q26.31) WILD-TYPE 84 45
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            13                            129 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             9                             45 
$`DEL PEAK 10(3Q26.31) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GM TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A4OH 
       25.78        14.30        13.94        25.41        25.28        19.50 
TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NW TCGA-R6-A6DN TCGA-RE-A7BO 
        7.43         3.95        12.92        46.09         8.02         7.00 
TCGA-VR-A8EU 
       18.31 

$`DEL PEAK 10(3Q26.31) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.46         0.43       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
        3.68        41.52        42.77        15.48        23.18        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       17.59         6.21         3.16         3.45         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-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         0.36         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.42        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        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-A49V 
        0.07         0.33         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-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.20         1.18        17.62         5.16         3.78         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-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         8.78        14.01         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.48         8.15         4.44         8.12        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          3.95                           0.03 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                         46.09                         122.10 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                         14.30                           7.04 
[1] "4.0 - 46.1 (14.3)" "0.0 - 122.1 (7.0)"
[1] "hr=" "1.4"
D41V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3Q26.31) MUTATED         1        0        1        0         0
  DEL PEAK 10(3Q26.31) WILD-TYPE       7        4        5        1        35
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3Q26.31) MUTATED           4         2          0          0
  DEL PEAK 10(3Q26.31) WILD-TYPE        22        21         11          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 10(3Q26.31) MUTATED            1        2         0
  DEL PEAK 10(3Q26.31) WILD-TYPE          5        1         2
D41V3, multiclass
            clus
vv           DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              0                              4
  STAGE IB                              1                              5
  STAGE II                              0                              1
  STAGE IIA                             0                             35
  STAGE IIB                             4                             22
  STAGE III                             2                             21
  STAGE IIIA                            0                             11
  STAGE IIIB                            0                              8
  STAGE IIIC                            1                              5
  STAGE IV                              2                              1
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 10(3Q26.31) MUTATED       5  3  4  0
  DEL PEAK 10(3Q26.31) WILD-TYPE    21 30 70  4
D41V4, multiclass
       clus
vv      DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  T0+T1                            5                             21
  T2                               3                             30
  T3                               4                             70
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 10(3Q26.31) MUTATED    3  8  0  1
  DEL PEAK 10(3Q26.31) WILD-TYPE 61 46 11  5
D41V5, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  N0                            3                             61
  N1                            8                             46
  N2                            0                             11
  N3                            1                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 10(3Q26.31) MUTATED    10   2   0   0
  DEL PEAK 10(3Q26.31) WILD-TYPE 101   0   3  17
D41V6, multiclass
     clus
vv    DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  M0                            10                            101
  M1                             2                              0
  M1A                            0                              3
  MX                             0                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED     1  12
  DEL PEAK 10(3Q26.31) WILD-TYPE  20 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      1   12
  DEL PEAK 10(3Q26.31) WILD-TYPE   20  117
        clus
vv       DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  FEMALE                            1                             20
  MALE                             12                            117
[1] 2 2
[1] FALSE
D41V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3Q26.31) MUTATED       0                         0    10
  DEL PEAK 10(3Q26.31) WILD-TYPE    38                         2    83
D41V9, multiclass
                           clus
vv                          DEL PEAK 10(3Q26.31) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               10
                           clus
vv                          DEL PEAK 10(3Q26.31) WILD-TYPE
  ASIAN                                                 38
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = DEL PEAK 11(4P15.2) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(4P15.2) MUTATED   46 36
  DEL PEAK 11(4P15.2) WILD-TYPE 42 18
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           82                            60 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           36                            18 
$`DEL PEAK 11(4P15.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.78        20.12         0.03         0.26         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH 
        0.36         0.13         0.46        44.75        60.39        42.77 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OJ 
       18.08         3.16         8.94         3.52         3.35         6.41 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        4.08         3.32         3.16         4.90         7.13         7.43 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         3.95        35.97        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       13.22         5.42         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49R TCGA-LN-A49U 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-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-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.59         5.06         7.04         6.35         9.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
       14.01         3.42         4.80         8.15         4.44        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I 
        8.12        36.72        12.03        15.91 

$`DEL PEAK 11(4P15.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
       31.27         7.63         2.63         0.99        17.03        23.41 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         0.43       122.10        68.02         3.68        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        15.48        23.18        25.28        17.59         6.21 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        3.45         0.30         4.31         3.68        19.50         8.78 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S 
       18.35         7.17         1.38        30.74        29.00         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE 
        8.71         2.60        25.12         0.36         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49O 
        2.66        13.48         7.76        21.37        83.24         0.33 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 
        0.13         0.10         0.07         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG 
        0.10        17.62         5.16         3.78        14.70        29.59 
TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-AA7D TCGA-ZR-A9CJ 
       53.95         8.78         5.29         8.48         9.17        18.12 

  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 
                        7.085                         8.595 
[1] "0.0 - 60.4 (7.1)"  "0.1 - 122.1 (8.6)"
[1] "hr=" "1.9"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4P15.2) MUTATED         4        2        4        1        20
  DEL PEAK 11(4P15.2) WILD-TYPE       4        2        2        0        15
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4P15.2) MUTATED          13        13          7          5
  DEL PEAK 11(4P15.2) WILD-TYPE        13        10          4          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 11(4P15.2) MUTATED            2        3         1
  DEL PEAK 11(4P15.2) WILD-TYPE          4        0         1
D42V3, multiclass
            clus
vv           DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             2                             2
  STAGE IB                             4                             2
  STAGE II                             1                             0
  STAGE IIA                           20                            15
  STAGE IIB                           13                            13
  STAGE III                           13                            10
  STAGE IIIA                           7                             4
  STAGE IIIB                           5                             3
  STAGE IIIC                           2                             4
  STAGE IV                             3                             0
  STAGE IVA                            1                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 11(4P15.2) MUTATED      12 21 41  3
  DEL PEAK 11(4P15.2) WILD-TYPE    14 12 33  1
D42V4, multiclass
       clus
vv      DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T0+T1                          12                            14
  T2                             21                            12
  T3                             41                            33
  T4                              3                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 11(4P15.2) MUTATED   36 32  7  2
  DEL PEAK 11(4P15.2) WILD-TYPE 28 22  4  4
D42V5, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                          36                            28
  N1                          32                            22
  N2                           7                             4
  N3                           2                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 11(4P15.2) MUTATED   67  2   2  4
  DEL PEAK 11(4P15.2) WILD-TYPE 44  0   1 13
D42V6, multiclass
     clus
vv    DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  M0                           67                            44
  M1                            2                             0
  M1A                           2                             1
  MX                            4                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED   12 75
  DEL PEAK 11(4P15.2) WILD-TYPE  9 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     12   75
  DEL PEAK 11(4P15.2) WILD-TYPE    9   54
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                          12                             9
  MALE                            75                            54
[1] 2 2
[1] FALSE
D42V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4P15.2) MUTATED      24                         1    50
  DEL PEAK 11(4P15.2) WILD-TYPE    14                         1    43
D42V9, multiclass
                           clus
vv                          DEL PEAK 11(4P15.2) MUTATED
  ASIAN                                              24
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              50
                           clus
vv                          DEL PEAK 11(4P15.2) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = DEL PEAK 12(4Q22.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 12(4Q22.1) MUTATED   45 37
  DEL PEAK 12(4Q22.1) WILD-TYPE 43 17
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           82                            60 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           37                            17 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 
        0.85         0.26         0.53         0.79         0.36         0.46 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C 
       44.75        60.39        42.77        23.18        18.08         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-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        2.60         7.40         3.95        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS 
       12.92        13.48        16.47        13.22         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       10.45         0.16         0.33         0.10         0.07         0.07 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.07         0.07         0.10         0.10         0.20         1.18 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW 
        9.30         7.00         8.78        14.01         4.80         8.15 
TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I 
        4.44        36.72        12.03        15.91 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
TCGA-2H-A9GJ TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       58.55        20.78         2.63        20.12         0.03         0.99 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 
       17.03        23.41         0.13        14.86         0.43       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        25.41        15.48        25.28 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       17.59         6.21         3.45         0.30         3.68        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OU 
        8.78         6.41         4.08        18.35         7.17        29.00 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NM 
        8.71        25.12         0.36         3.02        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X 
        5.42        21.37         0.07         0.13         0.10         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.13         0.10         0.10         0.07         0.07         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-V5-A7RB 
       17.62         5.16         3.78        14.70        53.95         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA7D TCGA-ZR-A9CJ 
        3.42         8.48        18.31         8.12         9.17        18.12 

  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                        7.510                         7.465 
[1] "0.1 - 83.2 (7.5)"  "0.0 - 122.1 (7.5)"
[1] "hr=" "1.6"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(4Q22.1) MUTATED         2        1        5        1        17
  DEL PEAK 12(4Q22.1) WILD-TYPE       6        3        1        0        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q22.1) MUTATED          14        17          7          5
  DEL PEAK 12(4Q22.1) WILD-TYPE        12         6          4          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 12(4Q22.1) MUTATED            2        2         2
  DEL PEAK 12(4Q22.1) WILD-TYPE          4        1         0
D43V3, multiclass
            clus
vv           DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             3
  STAGE IB                             5                             1
  STAGE II                             1                             0
  STAGE IIA                           17                            18
  STAGE IIB                           14                            12
  STAGE III                           17                             6
  STAGE IIIA                           7                             4
  STAGE IIIB                           5                             3
  STAGE IIIC                           2                             4
  STAGE IV                             2                             1
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 12(4Q22.1) MUTATED      10 20 45  2
  DEL PEAK 12(4Q22.1) WILD-TYPE    16 13 29  2
D43V4, multiclass
       clus
vv      DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T0+T1                          10                            16
  T2                             20                            13
  T3                             45                            29
  T4                              2                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 12(4Q22.1) MUTATED   32 35  8  2
  DEL PEAK 12(4Q22.1) WILD-TYPE 32 19  3  4
D43V5, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                          32                            32
  N1                          35                            19
  N2                           8                             3
  N3                           2                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 12(4Q22.1) MUTATED   63  1   3  9
  DEL PEAK 12(4Q22.1) WILD-TYPE 48  1   0  8
D43V6, multiclass
     clus
vv    DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  M0                           63                            48
  M1                            1                             1
  M1A                           3                             0
  MX                            9                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED   10 77
  DEL PEAK 12(4Q22.1) WILD-TYPE 11 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     10   77
  DEL PEAK 12(4Q22.1) WILD-TYPE   11   52
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                          10                            11
  MALE                            77                            52
[1] 2 2
[1] FALSE
D43V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q22.1) MUTATED      22                         0    52
  DEL PEAK 12(4Q22.1) WILD-TYPE    16                         2    41
D43V9, multiclass
                           clus
vv                          DEL PEAK 12(4Q22.1) MUTATED
  ASIAN                                              22
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              52
                           clus
vv                          DEL PEAK 12(4Q22.1) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                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"

Clustering(44) Variable = DEL PEAK 13(4Q34.3) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(4Q34.3) MUTATED   44 35
  DEL PEAK 13(4Q34.3) WILD-TYPE 44 19
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           79                            63 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           35                            19 
$`DEL PEAK 13(4Q34.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       32.45        33.27         0.85         0.26         0.53         0.79 
TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A6FH 
        0.36       122.10        44.75        60.39        41.52        42.77 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       23.18        18.08         3.16         4.31         8.94         3.52 
TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
        3.35        18.35         3.32         7.17         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-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.95        55.50         2.66        35.97        12.92        16.47 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22         5.42         8.71        13.41        27.12        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       46.09        10.36         0.07        10.45         0.16         0.33 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 
        0.10         0.07         0.07         0.10         0.10         0.20 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
        5.16         3.78         8.02         7.59         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
       29.59         6.35         9.30         7.00        14.01         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I 
        8.15         4.44         8.12        36.72        12.03        15.91 
TCGA-ZR-A9CJ 
       18.12 

$`DEL PEAK 13(4Q34.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A3YA 
       31.27        58.55         7.63        13.94        20.09        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
        2.63        20.12         0.03         0.99        17.03        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A6FE 
        0.13        14.86         0.46         0.43        68.02         3.68 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       25.41        15.48        25.28        17.59         6.21         3.45 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        0.30         3.68        19.50         8.78         6.41         4.08 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 
        1.38        29.00         8.71         2.60        25.12         3.02 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-LN-A49N 
       13.48        13.55         7.76        21.37        52.57         0.07 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.13         0.07         0.10         0.10         0.07         0.13 
TCGA-LN-A4A4 TCGA-LN-A4A5 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-R6-A6L4 TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
       17.62        14.70        53.95         8.78         5.29         3.42 
TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-AA7D 
        8.48        18.31         9.17 

  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                       122.10                         68.02 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                         7.43                          7.63 
[1] "0.1 - 122.1 (7.4)" "0.0 - 68.0 (7.6)" 
[1] "hr=" "1.3"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4Q34.3) MUTATED         3        2        5        1        13
  DEL PEAK 13(4Q34.3) WILD-TYPE       5        2        1        0        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4Q34.3) MUTATED          12        16          5          7
  DEL PEAK 13(4Q34.3) WILD-TYPE        14         7          6          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 13(4Q34.3) MUTATED            3        2         2
  DEL PEAK 13(4Q34.3) WILD-TYPE          3        1         0
D44V3, multiclass
            clus
vv           DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             2                             2
  STAGE IB                             5                             1
  STAGE II                             1                             0
  STAGE IIA                           13                            22
  STAGE IIB                           12                            14
  STAGE III                           16                             7
  STAGE IIIA                           5                             6
  STAGE IIIB                           7                             1
  STAGE IIIC                           3                             3
  STAGE IV                             2                             1
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 13(4Q34.3) MUTATED      12 18 42  2
  DEL PEAK 13(4Q34.3) WILD-TYPE    14 15 32  2
D44V4, multiclass
       clus
vv      DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  T0+T1                          12                            14
  T2                             18                            15
  T3                             42                            32
  T4                              2                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 13(4Q34.3) MUTATED   30 32  9  3
  DEL PEAK 13(4Q34.3) WILD-TYPE 34 22  2  3
D44V5, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  N0                          30                            34
  N1                          32                            22
  N2                           9                             2
  N3                           3                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 13(4Q34.3) MUTATED   59  1   3  9
  DEL PEAK 13(4Q34.3) WILD-TYPE 52  1   0  8
D44V6, multiclass
     clus
vv    DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  M0                           59                            52
  M1                            1                             1
  M1A                           3                             0
  MX                            9                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q34.3) MUTATED   12 72
  DEL PEAK 13(4Q34.3) WILD-TYPE  9 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     12   72
  DEL PEAK 13(4Q34.3) WILD-TYPE    9   57
        clus
vv       DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  FEMALE                          12                             9
  MALE                            72                            57
[1] 2 2
[1] FALSE
D44V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4Q34.3) MUTATED      20                         0    54
  DEL PEAK 13(4Q34.3) WILD-TYPE    18                         2    39
D44V9, multiclass
                           clus
vv                          DEL PEAK 13(4Q34.3) MUTATED
  ASIAN                                              20
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              54
                           clus
vv                          DEL PEAK 13(4Q34.3) WILD-TYPE
  ASIAN                                                18
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 14(5Q12.1) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(5Q12.1) MUTATED   54 33
  DEL PEAK 14(5Q12.1) WILD-TYPE 34 21
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                           87                            55 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                           33                            21 
$`DEL PEAK 14(5Q12.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 
        0.85         2.63         0.26         0.53        17.03         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
      122.10        44.75        60.39        42.77        25.28        18.08 
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-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       55.50         2.66        35.97        12.92        13.48        13.55 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
        5.42        21.37         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R 
       46.09        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 TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        8.78         3.42         8.15         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        15.91        18.12 

$`DEL PEAK 14(5Q12.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
       31.27        20.78        20.12         0.03         0.99         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6FD 
       23.41         0.36         0.13        14.86         0.43        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F 
        3.68        41.52        25.41        15.48        23.18        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4ON 
        6.21         3.16         0.30         8.94         8.78        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        1.38        29.00         7.43         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49M 
        7.40        16.47        13.22         7.76        83.24         0.16 
TCGA-LN-A49O TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
        0.33         0.10         0.07         0.10         0.10         0.07 
TCGA-LN-A4MR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.07         3.78         8.02         7.59        14.70         7.04 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-AA4G 
        7.00        14.01         5.29         4.80         8.48        12.03 
TCGA-VR-AA7D 
        9.17 

  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                       122.10                         83.24 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                         7.17                          7.59 
[1] "0.1 - 122.1 (7.2)" "0.0 - 83.2 (7.6)" 
[1] "hr=" "1.1"
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(5Q12.1) MUTATED         8        3        1        0        20
  DEL PEAK 14(5Q12.1) WILD-TYPE       0        1        5        1        15
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q12.1) MUTATED          14        16          6          5
  DEL PEAK 14(5Q12.1) WILD-TYPE        12         7          5          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 14(5Q12.1) MUTATED            4        3         2
  DEL PEAK 14(5Q12.1) WILD-TYPE          2        0         0
D45V3, multiclass
            clus
vv           DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  STAGE I                              8                             0
  STAGE IA                             3                             1
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           20                            15
  STAGE IIB                           14                            12
  STAGE III                           16                             7
  STAGE IIIA                           6                             5
  STAGE IIIB                           5                             3
  STAGE IIIC                           4                             2
  STAGE IV                             3                             0
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 14(5Q12.1) MUTATED      18 18 46  2
  DEL PEAK 14(5Q12.1) WILD-TYPE     8 15 28  2
D45V4, multiclass
       clus
vv      DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  T0+T1                          18                             8
  T2                             18                            15
  T3                             46                            28
  T4                              2                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 14(5Q12.1) MUTATED   40 35  5  4
  DEL PEAK 14(5Q12.1) WILD-TYPE 24 19  6  2
D45V5, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  N0                          40                            24
  N1                          35                            19
  N2                           5                             6
  N3                           4                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 14(5Q12.1) MUTATED   68  2   3  8
  DEL PEAK 14(5Q12.1) WILD-TYPE 43  0   0  9
D45V6, multiclass
     clus
vv    DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  M0                           68                            43
  M1                            2                             0
  M1A                           3                             0
  MX                            8                             9
[1] 4 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 14(5Q12.1) MUTATED   11 81
  DEL PEAK 14(5Q12.1) WILD-TYPE 10 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     11   81
  DEL PEAK 14(5Q12.1) WILD-TYPE   10   48
        clus
vv       DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  FEMALE                          11                            10
  MALE                            81                            48
[1] 2 2
[1] FALSE
D45V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q12.1) MUTATED      24                         1    54
  DEL PEAK 14(5Q12.1) WILD-TYPE    14                         1    39
D45V9, multiclass
                           clus
vv                          DEL PEAK 14(5Q12.1) MUTATED
  ASIAN                                              24
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              54
                           clus
vv                          DEL PEAK 14(5Q12.1) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(6P25.3) MUTATED   34 25
  DEL PEAK 15(6P25.3) WILD-TYPE 54 29
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           59                            83 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           25                            29 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       14.30        58.55         7.63        13.94         8.94         4.21 
TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 TCGA-JY-A6F8 
       33.27         0.03         0.26         0.53        23.41       122.10 
TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       60.39        23.18        25.28         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        4.31         3.35        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI 
        3.16         7.13         0.36         2.66        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       16.47        13.55        13.22        13.41        27.12        52.57 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 
       10.36         0.07         0.07         0.10         0.07         0.13 
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-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        9.30         8.78        14.01         5.29         3.42         8.48 
TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-ZR-A9CJ 
        8.15        18.31         8.12        12.03        18.12 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3QL 
       25.78        31.27         5.92        16.24        32.45        20.09 
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-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79         0.36         0.13        14.86         0.46         0.43 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       44.75        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OE 
       15.48        18.08        17.59         6.21         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OS 
        3.68        19.50         8.78         6.41         4.08        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
       25.12         7.40         3.95         3.02        55.50        12.92 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW 
        7.76         5.42        21.37         8.71        83.24        46.09 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45         0.16         0.33         0.10         0.13         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10         0.07         0.07         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         0.07         0.10         0.07         3.78         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO 
        5.06         7.04        29.59         6.35        53.95         7.00 
TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-VR-AA7I 
        4.80         4.44        36.72         9.17        15.91 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       122.10                         83.24 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         8.15                          7.00 
[1] "0.0 - 122.1 (8.2)" "0.1 - 83.2 (7.0)" 
[1] "hr=" "1.2"
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(6P25.3) MUTATED         5        2        1        0        11
  DEL PEAK 15(6P25.3) WILD-TYPE       3        2        5        1        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(6P25.3) MUTATED          11        10          4          4
  DEL PEAK 15(6P25.3) WILD-TYPE        15        13          7          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 15(6P25.3) MUTATED            4        1         1
  DEL PEAK 15(6P25.3) WILD-TYPE          2        2         1
D46V3, multiclass
            clus
vv           DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             2
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           11                            24
  STAGE IIB                           11                            15
  STAGE III                           10                            13
  STAGE IIIA                           4                             7
  STAGE IIIB                           4                             4
  STAGE IIIC                           4                             2
  STAGE IV                             1                             2
  STAGE IVA                            1                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 15(6P25.3) MUTATED      13 11 32  0
  DEL PEAK 15(6P25.3) WILD-TYPE    13 22 42  4
D46V4, multiclass
       clus
vv      DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T0+T1                          13                            13
  T2                             11                            22
  T3                             32                            42
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 15(6P25.3) MUTATED   26 20  6  4
  DEL PEAK 15(6P25.3) WILD-TYPE 38 34  5  2
D46V5, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          26                            38
  N1                          20                            34
  N2                           6                             5
  N3                           4                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 15(6P25.3) MUTATED   42  1   1 11
  DEL PEAK 15(6P25.3) WILD-TYPE 69  1   2  6
D46V6, multiclass
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  M0                           42                            69
  M1                            1                             1
  M1A                           1                             2
  MX                           11                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED    9 53
  DEL PEAK 15(6P25.3) WILD-TYPE 12 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      9   53
  DEL PEAK 15(6P25.3) WILD-TYPE   12   76
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                           9                            12
  MALE                            53                            76
[1] 2 2
[1] FALSE
D46V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6P25.3) MUTATED      12                         2    39
  DEL PEAK 15(6P25.3) WILD-TYPE    26                         0    54
D46V9, multiclass
                           clus
vv                          DEL PEAK 15(6P25.3) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              39
                           clus
vv                          DEL PEAK 15(6P25.3) WILD-TYPE
  ASIAN                                                26
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 16(6Q16.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 16(6Q16.3) MUTATED   28 12
  DEL PEAK 16(6Q16.3) WILD-TYPE 60 42
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           40                           102 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           12                            42 
$`DEL PEAK 16(6Q16.3) MUTATED`
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H 
       25.78        33.27        20.09         0.53         0.46         0.43 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M 
       44.75        60.39        42.77        18.08         3.16         8.94 
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       18.35         3.16         0.36        16.47        13.55        13.22 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W 
       13.41        83.24        52.57         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.10         0.10         0.07         0.20         1.18 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC 
        8.02         5.06        29.59         8.78        14.01         3.42 
TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-ZR-A9CJ 
        8.15        18.31         8.12        18.12 

$`DEL PEAK 16(6Q16.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94        16.24         4.21        32.45         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12         0.03         0.26         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 
        0.79        23.41         0.36         0.13        14.86       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       25.28        17.59         6.21         3.45         0.30         4.31 
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-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
        4.08         3.32         7.17         1.38        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       35.97        12.92        13.48         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        8.71        27.12        46.09        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-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-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       17.62         5.16         3.78         7.59        14.70         7.04 
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 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.48         4.44        36.72        12.03         9.17        15.91 

  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                        8.465                         7.150 
[1] "0.1 - 83.2 (8.5)"  "0.0 - 122.1 (7.2)"
[1] "hr=" "1.6"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(6Q16.3) MUTATED         1        1        1        0        11
  DEL PEAK 16(6Q16.3) WILD-TYPE       7        3        5        1        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6Q16.3) MUTATED           6         6          3          2
  DEL PEAK 16(6Q16.3) WILD-TYPE        20        17          8          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 16(6Q16.3) MUTATED            1        1         0
  DEL PEAK 16(6Q16.3) WILD-TYPE          5        2         2
D47V3, multiclass
            clus
vv           DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             1                             3
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           11                            24
  STAGE IIB                            6                            20
  STAGE III                            6                            17
  STAGE IIIA                           3                             8
  STAGE IIIB                           2                             6
  STAGE IIIC                           1                             5
  STAGE IV                             1                             2
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 16(6Q16.3) MUTATED       5  8 22  0
  DEL PEAK 16(6Q16.3) WILD-TYPE    21 25 52  4
D47V4, multiclass
       clus
vv      DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  T0+T1                           5                            21
  T2                              8                            25
  T3                             22                            52
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 16(6Q16.3) MUTATED   16 14  3  1
  DEL PEAK 16(6Q16.3) WILD-TYPE 48 40  8  5
D47V5, multiclass
    clus
vv   DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  N0                          16                            48
  N1                          14                            40
  N2                           3                             8
  N3                           1                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 16(6Q16.3) MUTATED   27  1   0  6
  DEL PEAK 16(6Q16.3) WILD-TYPE 84  1   3 11
D47V6, multiclass
     clus
vv    DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  M0                           27                            84
  M1                            1                             1
  M1A                           0                             3
  MX                            6                            11
[1] 4 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 16(6Q16.3) MUTATED    3 38
  DEL PEAK 16(6Q16.3) WILD-TYPE 18 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.3) MUTATED      3   38
  DEL PEAK 16(6Q16.3) WILD-TYPE   18   91
        clus
vv       DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  FEMALE                           3                            18
  MALE                            38                            91
[1] 2 2
[1] FALSE
D47V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q16.3) MUTATED      15                         1    23
  DEL PEAK 16(6Q16.3) WILD-TYPE    23                         1    70
D47V9, multiclass
                           clus
vv                          DEL PEAK 16(6Q16.3) MUTATED
  ASIAN                                              15
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              23
                           clus
vv                          DEL PEAK 16(6Q16.3) WILD-TYPE
  ASIAN                                                23
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 17(6Q26) MUTATION ANALYSIS
D48V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 17(6Q26) MUTATED   29 10
  DEL PEAK 17(6Q26) WILD-TYPE 59 44
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         39                         103 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         10                          44 
$`DEL PEAK 17(6Q26) MUTATED`
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FH 
       25.78        33.27        20.09         0.46         0.43        42.77 
TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OR 
       25.41        18.08         3.16         4.31         8.94         3.16 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        0.36         7.40        13.48        16.47        13.55        13.22 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W 
       13.41        83.24        52.57         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6XG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        1.18         8.02        29.59        14.01         3.42         4.80 
TCGA-V5-AASW TCGA-VR-A8EW TCGA-ZR-A9CJ 
        8.15         8.12        18.12 

$`DEL PEAK 17(6Q26) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94        16.24         4.21        32.45         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41         0.36         0.13        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       15.48        23.18        25.28        17.59         6.21         3.45 
TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        0.30         3.52         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-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-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        8.71         2.60        25.12         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        2.66        35.97        12.92         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        8.71        27.12        46.09        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 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        8.48         4.44        18.31        36.72        12.03         9.17 
TCGA-VR-AA7I 
       15.91 

  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                       0.07                        0.03 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                      83.24                      122.10 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                       8.02                        7.43 
[1] "0.1 - 83.2 (8.0)"  "0.0 - 122.1 (7.4)"
[1] "hr=" "1.6"
D48V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6Q26) MUTATED         0        1        2        0        15
  DEL PEAK 17(6Q26) WILD-TYPE       8        3        4        1        20
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q26) MUTATED           5         8          1          2
  DEL PEAK 17(6Q26) WILD-TYPE        21        15         10          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 17(6Q26) MUTATED            1        0         0
  DEL PEAK 17(6Q26) WILD-TYPE          5        3         2
D48V3, multiclass
            clus
vv           DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  STAGE I                            0                           8
  STAGE IA                           1                           3
  STAGE IB                           2                           4
  STAGE II                           0                           1
  STAGE IIA                         15                          20
  STAGE IIB                          5                          21
  STAGE III                          8                          15
  STAGE IIIA                         1                          10
  STAGE IIIB                         2                           6
  STAGE IIIC                         1                           5
  STAGE IV                           0                           3
  STAGE IVA                          0                           2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 17(6Q26) MUTATED       4  8 25  0
  DEL PEAK 17(6Q26) WILD-TYPE    22 25 49  4
D48V4, multiclass
       clus
vv      DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  T0+T1                         4                          22
  T2                            8                          25
  T3                           25                          49
  T4                            0                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 17(6Q26) MUTATED   21 11  3  1
  DEL PEAK 17(6Q26) WILD-TYPE 43 43  8  5
D48V5, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  N0                        21                          43
  N1                        11                          43
  N2                         3                           8
  N3                         1                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 M1A MX
  DEL PEAK 17(6Q26) MUTATED   31  0   0  6
  DEL PEAK 17(6Q26) WILD-TYPE 80  2   3 11
D48V6, multiclass
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  M0                         31                          80
  M1                          0                           2
  M1A                         0                           3
  MX                          6                          11
[1] 4 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 17(6Q26) MUTATED    4 38
  DEL PEAK 17(6Q26) WILD-TYPE 17 91
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      4   38
  DEL PEAK 17(6Q26) WILD-TYPE   17   91
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                         4                          17
  MALE                          38                          91
[1] 2 2
[1] FALSE
D48V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6Q26) MUTATED      16                         1    23
  DEL PEAK 17(6Q26) WILD-TYPE    22                         1    70
D48V9, multiclass
                           clus
vv                          DEL PEAK 17(6Q26) MUTATED
  ASIAN                                            16
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            23
                           clus
vv                          DEL PEAK 17(6Q26) WILD-TYPE
  ASIAN                                              22
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = DEL PEAK 18(7Q31.1) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 18(7Q31.1) MUTATED   28 20
  DEL PEAK 18(7Q31.1) WILD-TYPE 60 34
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           48                            94 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           20                            34 
$`DEL PEAK 18(7Q31.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78        14.30         7.63         5.92         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A51D 
       32.45         0.85         2.63        20.12         0.26        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OF 
        0.79         0.13         0.46        42.77         3.16         3.68 
TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.08         3.16        29.00         6.94         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        0.36        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49W 
       13.55         8.71        10.36         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-M9-A5M8 
        0.10         0.07         0.07         0.10         0.07        17.62 
TCGA-R6-A6KZ TCGA-V5-A7RB TCGA-V5-AASX TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        5.06         5.29         4.44        12.03         9.17        15.91 

$`DEL PEAK 18(7Q31.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL 
       31.27        58.55        13.94        16.24        33.27        20.09 
TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 
       20.78         0.03         0.99         0.53        23.41         0.36 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         0.43       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       18.08        17.59         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-A8NG TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS 
       35.97        13.22         7.76         5.42        21.37        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L 
       27.12        83.24        52.57        46.09         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 
        0.16         0.33         0.13         0.07         0.10         0.13 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 
        0.10         0.10         0.07         0.07         0.10         0.20 
TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
        1.18         5.16         3.78         8.02         7.59        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-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        8.78        14.01         3.42         4.80         8.48         8.15 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
       18.31         8.12        36.72        18.12 

  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         55.5                         122.1 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        5.175                         8.070 
[1] "0.1 - 55.5 (5.2)"  "0.0 - 122.1 (8.1)"
[1] "hr=" "1.7"
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(7Q31.1) MUTATED         0        2        2        1         8
  DEL PEAK 18(7Q31.1) WILD-TYPE       8        2        4        0        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(7Q31.1) MUTATED           6        14          4          2
  DEL PEAK 18(7Q31.1) WILD-TYPE        20         9          7          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 18(7Q31.1) MUTATED            2        1         1
  DEL PEAK 18(7Q31.1) WILD-TYPE          4        2         1
D49V3, multiclass
            clus
vv           DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  STAGE I                              0                             8
  STAGE IA                             2                             2
  STAGE IB                             2                             4
  STAGE II                             1                             0
  STAGE IIA                            8                            27
  STAGE IIB                            6                            20
  STAGE III                           14                             9
  STAGE IIIA                           4                             7
  STAGE IIIB                           2                             6
  STAGE IIIC                           2                             4
  STAGE IV                             1                             2
  STAGE IVA                            1                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 18(7Q31.1) MUTATED       8  7 28  2
  DEL PEAK 18(7Q31.1) WILD-TYPE    18 26 46  2
D49V4, multiclass
       clus
vv      DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  T0+T1                           8                            18
  T2                              7                            26
  T3                             28                            46
  T4                              2                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 18(7Q31.1) MUTATED   18 22  3  2
  DEL PEAK 18(7Q31.1) WILD-TYPE 46 32  8  4
D49V5, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  N0                          18                            46
  N1                          22                            32
  N2                           3                             8
  N3                           2                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 18(7Q31.1) MUTATED   34  1   1  7
  DEL PEAK 18(7Q31.1) WILD-TYPE 77  1   2 10
D49V6, multiclass
     clus
vv    DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  M0                           34                            77
  M1                            1                             1
  M1A                           1                             2
  MX                            7                            10
[1] 4 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 18(7Q31.1) MUTATED    4 44
  DEL PEAK 18(7Q31.1) WILD-TYPE 17 85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      4   44
  DEL PEAK 18(7Q31.1) WILD-TYPE   17   85
        clus
vv       DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  FEMALE                           4                            17
  MALE                            44                            85
[1] 2 2
[1] FALSE
D49V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(7Q31.1) MUTATED       9                         0    28
  DEL PEAK 18(7Q31.1) WILD-TYPE    29                         2    65
D49V9, multiclass
                           clus
vv                          DEL PEAK 18(7Q31.1) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              28
                           clus
vv                          DEL PEAK 18(7Q31.1) WILD-TYPE
  ASIAN                                                29
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = DEL PEAK 19(7Q36.3) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 19(7Q36.3) MUTATED   33 24
  DEL PEAK 19(7Q36.3) WILD-TYPE 55 30
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           57                            85 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           24                            30 
$`DEL PEAK 19(7Q36.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        14.30         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5B8 
        4.21         0.85        20.12         0.03        17.03         0.79 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
        0.13         0.43        44.75        68.02         3.68        42.77 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       18.08         3.16         3.68         4.08        18.35         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        3.16        30.74        29.00         7.13         6.94         0.36 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NR 
       55.50         2.66        12.92        13.48        13.55         8.71 
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-AASX 
       17.62         3.78         5.06        29.59         5.29         4.44 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.03         9.17        15.91 

$`DEL PEAK 19(7Q36.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
       31.27        58.55        13.94        32.45        33.27        20.09 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 
       20.78         2.63         0.26         0.99         0.53        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FG 
        0.36        14.86         0.46       122.10        60.39        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        15.48        23.18        25.28        17.59         6.21 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
        3.45         0.30         4.31         8.94         3.52         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OT 
       19.50         8.78         6.41         3.32         1.38         4.90 
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-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02        35.97        16.47        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        0.07         0.16         0.07         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 
        0.13         0.10         0.10         0.07         0.07         0.20 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        5.16         8.02         7.59        14.70         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC 
       53.95         9.30         7.00         8.78        14.01         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 
        4.80         8.48         8.15        18.31         8.12        36.72 
TCGA-ZR-A9CJ 
       18.12 

  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                         6.94                          8.02 
[1] "0.0 - 68.0 (6.9)"  "0.1 - 122.1 (8.0)"
[1] "hr=" "1.5"
D50V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(7Q36.3) MUTATED         0        3        2        1        13
  DEL PEAK 19(7Q36.3) WILD-TYPE       8        1        4        0        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(7Q36.3) MUTATED          10        13          4          1
  DEL PEAK 19(7Q36.3) WILD-TYPE        16        10          7          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 19(7Q36.3) MUTATED            2        1         2
  DEL PEAK 19(7Q36.3) WILD-TYPE          4        2         0
D50V3, multiclass
            clus
vv           DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  STAGE I                              0                             8
  STAGE IA                             3                             1
  STAGE IB                             2                             4
  STAGE II                             1                             0
  STAGE IIA                           13                            22
  STAGE IIB                           10                            16
  STAGE III                           13                            10
  STAGE IIIA                           4                             7
  STAGE IIIB                           1                             7
  STAGE IIIC                           2                             4
  STAGE IV                             1                             2
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 19(7Q36.3) MUTATED      10 12 30  2
  DEL PEAK 19(7Q36.3) WILD-TYPE    16 21 44  2
D50V4, multiclass
       clus
vv      DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  T0+T1                          10                            16
  T2                             12                            21
  T3                             30                            44
  T4                              2                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 19(7Q36.3) MUTATED   23 26  2  2
  DEL PEAK 19(7Q36.3) WILD-TYPE 41 28  9  4
D50V5, multiclass
    clus
vv   DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  N0                          23                            41
  N1                          26                            28
  N2                           2                             9
  N3                           2                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 19(7Q36.3) MUTATED   42  1   2  6
  DEL PEAK 19(7Q36.3) WILD-TYPE 69  1   1 11
D50V6, multiclass
     clus
vv    DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  M0                           42                            69
  M1                            1                             1
  M1A                           2                             1
  MX                            6                            11
[1] 4 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 19(7Q36.3) MUTATED    8 50
  DEL PEAK 19(7Q36.3) WILD-TYPE 13 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED      8   50
  DEL PEAK 19(7Q36.3) WILD-TYPE   13   79
        clus
vv       DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  FEMALE                           8                            13
  MALE                            50                            79
[1] 2 2
[1] FALSE
D50V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(7Q36.3) MUTATED      15                         0    31
  DEL PEAK 19(7Q36.3) WILD-TYPE    23                         2    62
D50V9, multiclass
                           clus
vv                          DEL PEAK 19(7Q36.3) MUTATED
  ASIAN                                              15
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              31
                           clus
vv                          DEL PEAK 19(7Q36.3) WILD-TYPE
  ASIAN                                                23
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK 20(8P23.2) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 20(8P23.2) MUTATED   45 25
  DEL PEAK 20(8P23.2) WILD-TYPE 43 29
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           70                            72 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           25                            29 
$`DEL PEAK 20(8P23.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3Y9 
       25.78        31.27         5.92        13.94         4.21         0.85 
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-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
       23.41         0.13         0.43        44.75        60.39         3.68 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        23.18        25.28        18.08        17.59 
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-L5-A8NF TCGA-L5-A8NL 
        7.43         2.60         7.40         3.95         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L 
        5.42         8.71        13.41        27.12        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-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW 
        3.42         4.80         8.48         8.15        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       36.72        12.03         9.17        15.91 

$`DEL PEAK 20(8P23.2) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       14.30        58.55         7.63         8.94        16.24        32.45 
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-JY-A939 
       14.86         0.46       122.10        68.02        41.52        15.48 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG 
        6.21         3.16         3.45         0.30         8.94         3.35 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         6.41         4.08        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T 
        3.16        30.74        29.00         7.13         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH 
       25.12         0.36         3.02        55.50        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.48        16.47        13.55         7.76        21.37        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       52.57        46.09         0.07         0.33         0.10         0.07 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.10         0.10         0.10         0.10         0.07         0.07 
TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       17.62         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-AASX TCGA-ZR-A9CJ 
        6.35         9.30         7.00         8.78         4.44        18.12 

  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                        60.39                        122.10 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                        5.355                         8.745 
[1] "0.0 - 60.4 (5.4)"  "0.1 - 122.1 (8.7)"
[1] "hr=" "1.2"
D51V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(8P23.2) MUTATED         2        0        4        0        12
  DEL PEAK 20(8P23.2) WILD-TYPE       6        4        2        1        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8P23.2) MUTATED          17        12          6          6
  DEL PEAK 20(8P23.2) WILD-TYPE         9        11          5          2
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 20(8P23.2) MUTATED            4        2         1
  DEL PEAK 20(8P23.2) WILD-TYPE          2        1         1
D51V3, multiclass
            clus
vv           DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             4
  STAGE IB                             4                             2
  STAGE II                             0                             1
  STAGE IIA                           12                            23
  STAGE IIB                           17                             9
  STAGE III                           12                            11
  STAGE IIIA                           6                             5
  STAGE IIIB                           6                             2
  STAGE IIIC                           4                             2
  STAGE IV                             2                             1
  STAGE IVA                            1                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 20(8P23.2) MUTATED      11 17 38  2
  DEL PEAK 20(8P23.2) WILD-TYPE    15 16 36  2
D51V4, multiclass
       clus
vv      DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  T0+T1                          11                            15
  T2                             17                            16
  T3                             38                            36
  T4                              2                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 20(8P23.2) MUTATED   25 31  7  4
  DEL PEAK 20(8P23.2) WILD-TYPE 39 23  4  2
D51V5, multiclass
    clus
vv   DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  N0                          25                            39
  N1                          31                            23
  N2                           7                             4
  N3                           4                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 20(8P23.2) MUTATED   57  1   2  6
  DEL PEAK 20(8P23.2) WILD-TYPE 54  1   1 11
D51V6, multiclass
     clus
vv    DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  M0                           57                            54
  M1                            1                             1
  M1A                           2                             1
  MX                            6                            11
[1] 4 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 20(8P23.2) MUTATED    6 66
  DEL PEAK 20(8P23.2) WILD-TYPE 15 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.2) MUTATED      6   66
  DEL PEAK 20(8P23.2) WILD-TYPE   15   63
        clus
vv       DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  FEMALE                           6                            15
  MALE                            66                            63
[1] 2 2
[1] FALSE
D51V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(8P23.2) MUTATED      20                         2    42
  DEL PEAK 20(8P23.2) WILD-TYPE    18                         0    51
D51V9, multiclass
                           clus
vv                          DEL PEAK 20(8P23.2) MUTATED
  ASIAN                                              20
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              42
                           clus
vv                          DEL PEAK 20(8P23.2) WILD-TYPE
  ASIAN                                                18
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 21(8P12) MUTATION ANALYSIS
D52V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 21(8P12) MUTATED   37 22
  DEL PEAK 21(8P12) WILD-TYPE 51 32
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         59                          83 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         22                          32 
$`DEL PEAK 21(8P12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3Y9 
       25.78        31.27         5.92        13.94         4.21         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63        20.12         0.03         0.53         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 
        0.13         0.43        44.75        60.39        42.77        25.41 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OH TCGA-L5-A4OJ 
       23.18        18.08         4.31         3.52        19.50         6.41 
TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        3.32         7.43         7.40         3.95        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-LN-A49L 
       13.48         5.42         8.71        13.41        27.12        10.45 
TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 
        0.07         0.13         0.07         0.07         0.13         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         0.10         0.07         0.20         3.78         8.02 
TCGA-R6-A6XG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EU 
       29.59         7.00         5.29         3.42         4.80        18.31 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        12.03         9.17        15.91        18.12 

$`DEL PEAK 21(8P12) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       14.30        58.55         7.63         8.94        16.24        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       33.27        20.09        20.78         0.26         0.99        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
        0.36        14.86         0.46       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       41.52        15.48        25.28        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
        3.45         0.30         8.94         3.68         3.35         8.78 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        4.08        18.35         7.17         1.38         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
       25.12         0.36         3.02        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV 
       13.55        13.22         7.76        21.37        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R 
       46.09        10.36         0.07         0.16         0.33         0.10 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.07         0.10         0.10         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         1.18        17.62         5.16         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV 
       14.70         7.04         6.35        53.95         9.30         8.78 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW 
       14.01         8.48         8.15         4.44         8.12 

  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                       0.03                        0.07 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                      60.39                      122.10 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                       6.41                        8.12 
[1] "0.0 - 60.4 (6.4)"  "0.1 - 122.1 (8.1)"
[1] "hr=" "1.2"
D52V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(8P12) MUTATED         3        0        2        0        10
  DEL PEAK 21(8P12) WILD-TYPE       5        4        4        1        25
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(8P12) MUTATED          16         9          7          3
  DEL PEAK 21(8P12) WILD-TYPE        10        14          4          5
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 21(8P12) MUTATED            3        1         1
  DEL PEAK 21(8P12) WILD-TYPE          3        2         1
D52V3, multiclass
            clus
vv           DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  STAGE I                            3                           5
  STAGE IA                           0                           4
  STAGE IB                           2                           4
  STAGE II                           0                           1
  STAGE IIA                         10                          25
  STAGE IIB                         16                          10
  STAGE III                          9                          14
  STAGE IIIA                         7                           4
  STAGE IIIB                         3                           5
  STAGE IIIC                         3                           3
  STAGE IV                           1                           2
  STAGE IVA                          1                           1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 21(8P12) MUTATED      11 14 30  2
  DEL PEAK 21(8P12) WILD-TYPE    15 19 44  2
D52V4, multiclass
       clus
vv      DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  T0+T1                        11                          15
  T2                           14                          19
  T3                           30                          44
  T4                            2                           2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 21(8P12) MUTATED   21 28  4  3
  DEL PEAK 21(8P12) WILD-TYPE 43 26  7  3
D52V5, multiclass
    clus
vv   DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  N0                        21                          43
  N1                        28                          26
  N2                         4                           7
  N3                         3                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 M1A MX
  DEL PEAK 21(8P12) MUTATED   51  1   1  3
  DEL PEAK 21(8P12) WILD-TYPE 60  1   2 14
D52V6, multiclass
     clus
vv    DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  M0                         51                          60
  M1                          1                           1
  M1A                         1                           2
  MX                          3                          14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                             cls
clus                           0  1
  DEL PEAK 21(8P12) MUTATED    6 54
  DEL PEAK 21(8P12) WILD-TYPE 15 75
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(8P12) MUTATED      6   54
  DEL PEAK 21(8P12) WILD-TYPE   15   75
        clus
vv       DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  FEMALE                         6                          15
  MALE                          54                          75
[1] 2 2
[1] FALSE
D52V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(8P12) MUTATED      16                         1    35
  DEL PEAK 21(8P12) WILD-TYPE    22                         1    58
D52V9, multiclass
                           clus
vv                          DEL PEAK 21(8P12) MUTATED
  ASIAN                                            16
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            35
                           clus
vv                          DEL PEAK 21(8P12) WILD-TYPE
  ASIAN                                              22
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 22(9P23) MUTATION ANALYSIS
D53V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 22(9P23) MUTATED   50 29
  DEL PEAK 22(9P23) WILD-TYPE 38 25
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                         79                          63 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                         29                          25 
$`DEL PEAK 22(9P23) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        4.21        32.45        20.12         0.03         0.26         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB 
        0.79        23.41         0.46         0.43        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H 
       68.02        25.41        25.28        18.08         3.16         0.30 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        8.94         3.68        19.50        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16        30.74         7.13         7.43         6.94         2.60 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.95        55.50         2.66        35.97        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       13.22         8.71        13.41        83.24        10.45         0.16 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.10         0.07         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.07         0.10         0.10         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XG 
        0.20         1.18        17.62         5.16         5.06        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        6.35         9.30         8.78        14.01         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 
        4.80         8.15         4.44        18.31         8.12        36.72 
TCGA-ZR-A9CJ 
       18.12 

$`DEL PEAK 22(9P23) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       58.55         5.92        13.94        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         2.63         0.99        17.03         0.36         0.13 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       14.86       122.10         3.68        41.52        42.77        15.48 
TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OE 
       23.18        17.59         6.21         3.45         4.31         3.52 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OT 
        3.35         8.78         6.41         4.08         1.38         4.90 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
       29.00         8.71        25.12         0.36         7.40         3.02 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT 
       12.92        13.55         7.76         5.42        21.37        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09        10.36         0.07         0.07         0.33 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13         0.10         0.10         0.07         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-V5-AASV 
        7.59        14.70         7.04        53.95         7.00         8.48 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.03         9.17        15.91 

  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                       0.03                        0.07 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                      83.24                      122.10 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                       7.17                        7.76 
[1] "0.0 - 83.2 (7.2)"  "0.1 - 122.1 (7.8)"
[1] "hr=" "1"  
D53V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(9P23) MUTATED         2        2        4        1        21
  DEL PEAK 22(9P23) WILD-TYPE       6        2        2        0        14
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(9P23) MUTATED          13        17          5          4
  DEL PEAK 22(9P23) WILD-TYPE        13         6          6          4
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 22(9P23) MUTATED            3        1         2
  DEL PEAK 22(9P23) WILD-TYPE          3        2         0
D53V3, multiclass
            clus
vv           DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  STAGE I                            2                           6
  STAGE IA                           2                           2
  STAGE IB                           4                           2
  STAGE II                           1                           0
  STAGE IIA                         21                          14
  STAGE IIB                         13                          13
  STAGE III                         17                           6
  STAGE IIIA                         5                           6
  STAGE IIIB                         4                           4
  STAGE IIIC                         3                           3
  STAGE IV                           1                           2
  STAGE IVA                          2                           0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 22(9P23) MUTATED      11 21 46  0
  DEL PEAK 22(9P23) WILD-TYPE    15 12 28  4
D53V4, multiclass
       clus
vv      DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  T0+T1                        11                          15
  T2                           21                          12
  T3                           46                          28
  T4                            0                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 22(9P23) MUTATED   33 36  5  3
  DEL PEAK 22(9P23) WILD-TYPE 31 18  6  3
D53V5, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  N0                        33                          31
  N1                        36                          18
  N2                         5                           6
  N3                         3                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 M1A MX
  DEL PEAK 22(9P23) MUTATED   64  1   2  9
  DEL PEAK 22(9P23) WILD-TYPE 47  1   1  8
D53V6, multiclass
     clus
vv    DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  M0                         64                          47
  M1                          1                           1
  M1A                         2                           1
  MX                          9                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED    8 78
  DEL PEAK 22(9P23) WILD-TYPE 13 51
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED      8   78
  DEL PEAK 22(9P23) WILD-TYPE   13   51
        clus
vv       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  FEMALE                         8                          13
  MALE                          78                          51
[1] 2 2
[1] FALSE
D53V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9P23) MUTATED      28                         1    44
  DEL PEAK 22(9P23) WILD-TYPE    10                         1    49
D53V9, multiclass
                           clus
vv                          DEL PEAK 22(9P23) MUTATED
  ASIAN                                            28
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            44
                           clus
vv                          DEL PEAK 22(9P23) WILD-TYPE
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 23(9P21.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 23(9P21.3) MUTATED   67 37
  DEL PEAK 23(9P21.3) WILD-TYPE 21 17
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          104                            38 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                           37                            17 
$`DEL PEAK 23(9P21.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        32.45        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         0.03         0.26         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA 
       23.41         0.36         0.13         0.46         0.43        44.75 
TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H 
       60.39        25.41        23.18        18.08         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
        4.31         8.94         3.68        19.50         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         7.17        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        7.43         6.94         2.60         0.36         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        35.97        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.42        21.37         8.71        13.41        83.24 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         0.07        10.45         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.10         0.13         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-M9-A5M8 
        0.07         0.10         0.07         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         3.78         5.06        14.70        29.59         6.35 
TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         8.78        14.01         5.29         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D 
        8.15         4.44        18.31         8.12        12.03         9.17 
TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.91        18.12 

$`DEL PEAK 23(9P21.3) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A4QT TCGA-IG-A7DP 
       58.55         5.92        13.94        20.09         0.99        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        42.77        15.48 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OG 
       25.28        17.59         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-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
        7.40        13.48         7.76        27.12        52.57        46.09 
TCGA-LN-A49V TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-RE-A7BO 
        0.10         8.02         7.59         7.04        53.95         7.00 
TCGA-V5-AASV TCGA-VR-A8Q7 
        8.48        36.72 

  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 
                        5.885                         8.745 
[1] "0.0 - 83.2 (5.9)"  "0.1 - 122.1 (8.7)"
[1] "hr=" "1.3"
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P21.3) MUTATED         3        2        4        1        29
  DEL PEAK 23(9P21.3) WILD-TYPE       5        2        2        0         6
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9P21.3) MUTATED          17        19          8          7
  DEL PEAK 23(9P21.3) WILD-TYPE         9         4          3          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 23(9P21.3) MUTATED            4        3         2
  DEL PEAK 23(9P21.3) WILD-TYPE          2        0         0
D54V3, multiclass
            clus
vv           DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             2                             2
  STAGE IB                             4                             2
  STAGE II                             1                             0
  STAGE IIA                           29                             6
  STAGE IIB                           17                             9
  STAGE III                           19                             4
  STAGE IIIA                           8                             3
  STAGE IIIB                           7                             1
  STAGE IIIC                           4                             2
  STAGE IV                             3                             0
  STAGE IVA                            2                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 23(9P21.3) MUTATED      15 26 59  3
  DEL PEAK 23(9P21.3) WILD-TYPE    11  7 15  1
D54V4, multiclass
       clus
vv      DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  T0+T1                          15                            11
  T2                             26                             7
  T3                             59                            15
  T4                              3                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 23(9P21.3) MUTATED   48 41  9  4
  DEL PEAK 23(9P21.3) WILD-TYPE 16 13  2  2
D54V5, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  N0                          48                            16
  N1                          41                            13
  N2                           9                             2
  N3                           4                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 23(9P21.3) MUTATED   84  2   3 11
  DEL PEAK 23(9P21.3) WILD-TYPE 27  0   0  6
D54V6, multiclass
     clus
vv    DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  M0                           84                            27
  M1                            2                             0
  M1A                           3                             0
  MX                           11                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED    12 100
  DEL PEAK 23(9P21.3) WILD-TYPE   9  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     12  100
  DEL PEAK 23(9P21.3) WILD-TYPE    9   29
        clus
vv       DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  FEMALE                          12                             9
  MALE                           100                            29
[1] 2 2
[1] FALSE
D54V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(9P21.3) MUTATED      36                         1    61
  DEL PEAK 23(9P21.3) WILD-TYPE     2                         1    32
D54V9, multiclass
                           clus
vv                          DEL PEAK 23(9P21.3) MUTATED
  ASIAN                                              36
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              61
                           clus
vv                          DEL PEAK 23(9P21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = DEL PEAK 24(10P15.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(10P15.3) MUTATED   23 16
  DEL PEAK 24(10P15.3) WILD-TYPE 65 38
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            39                            103 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            16                             38 
$`DEL PEAK 24(10P15.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 
       25.78        14.30         5.92         4.21        33.27         0.85 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C 
        0.03         0.53         0.79        23.41         0.43        23.18 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO 
        0.30         4.31         8.94         3.52         3.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A88V TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        3.16         4.90         2.60        13.41        27.12        83.24 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.07         0.33         0.07         0.10         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6Y0 TCGA-V5-A7RB TCGA-V5-A7RC 
        0.07         1.18         3.78        53.95         5.29         3.42 
TCGA-V5-A7RE TCGA-VR-A8EW TCGA-VR-AA4G 
        4.80         8.12        12.03 

$`DEL PEAK 24(10P15.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       32.45        20.09        20.78         2.63        20.12         0.26 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.99        17.03         0.36         0.13        14.86         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        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        15.48        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        6.21         3.16         3.45         3.68        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        6.41         4.08        18.35         7.17         1.38        30.74 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
       29.00         7.13         7.43         6.94         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         5.42        21.37         8.71        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S 
       10.36        10.45         0.16         0.07         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.10         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 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-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV 
        6.35         9.30         7.00         8.78        14.01         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-VR-AA7I 
        8.15         4.44        18.31        36.72         9.17        15.91 
TCGA-ZR-A9CJ 
       18.12 

  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                          3.52                           8.71 
[1] "0.0 - 83.2 (3.5)"  "0.1 - 122.1 (8.7)"
[1] "hr=" "1.7"
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(10P15.3) MUTATED         1        1        2        0        10
  DEL PEAK 24(10P15.3) WILD-TYPE       7        3        4        1        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10P15.3) MUTATED           5         9          3          4
  DEL PEAK 24(10P15.3) WILD-TYPE        21        14          8          4
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(10P15.3) MUTATED            1        1         0
  DEL PEAK 24(10P15.3) WILD-TYPE          5        2         2
D55V3, multiclass
            clus
vv           DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              1                              3
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                            10                             25
  STAGE IIB                             5                             21
  STAGE III                             9                             14
  STAGE IIIA                            3                              8
  STAGE IIIB                            4                              4
  STAGE IIIC                            1                              5
  STAGE IV                              1                              2
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 24(10P15.3) MUTATED       4  8 26  1
  DEL PEAK 24(10P15.3) WILD-TYPE    22 25 48  3
D55V4, multiclass
       clus
vv      DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  T0+T1                            4                             22
  T2                               8                             25
  T3                              26                             48
  T4                               1                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 24(10P15.3) MUTATED   18 13  6  1
  DEL PEAK 24(10P15.3) WILD-TYPE 46 41  5  5
D55V5, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  N0                           18                             46
  N1                           13                             41
  N2                            6                              5
  N3                            1                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 24(10P15.3) MUTATED   32  0   1  5
  DEL PEAK 24(10P15.3) WILD-TYPE 79  2   2 12
D55V6, multiclass
     clus
vv    DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  M0                            32                             79
  M1                             0                              2
  M1A                            1                              2
  MX                             5                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(10P15.3) MUTATED    5 36
  DEL PEAK 24(10P15.3) WILD-TYPE 16 93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED      5   36
  DEL PEAK 24(10P15.3) WILD-TYPE   16   93
        clus
vv       DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  FEMALE                            5                             16
  MALE                             36                             93
[1] 2 2
[1] FALSE
D55V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10P15.3) MUTATED      14                         1    20
  DEL PEAK 24(10P15.3) WILD-TYPE    24                         1    73
D55V9, multiclass
                           clus
vv                          DEL PEAK 24(10P15.3) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               20
                           clus
vv                          DEL PEAK 24(10P15.3) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK 25(10P11.21) MUTATION ANALYSIS
D56V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 25(10P11.21) MUTATED   19 15
  DEL PEAK 25(10P11.21) WILD-TYPE 69 39
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             34                             108 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             15                              39 
$`DEL PEAK 25(10P11.21) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YC 
       14.30         5.92        13.94        33.27         0.85        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
        0.03         0.53         0.79        23.41         0.43        44.75 
TCGA-JY-A6FE TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
        3.68        23.18         0.30         4.31         3.52         3.35 
TCGA-L5-A4OT TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49O 
        4.90        13.48        13.55        27.12        83.24         0.33 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.13         0.10         0.07         0.10         0.07         0.07 
TCGA-LN-A5U7 TCGA-V5-A7RC TCGA-VR-A8EW TCGA-VR-AA4G 
        1.18         3.42         8.12        12.03 

$`DEL PEAK 25(10P11.21) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS 
        4.21        32.45        20.09        20.78         2.63         0.26 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.99        17.03         0.36         0.13        14.86         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
      122.10        60.39        68.02        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.45         8.94         3.68        19.50         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-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       30.74        29.00         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-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        35.97        12.92        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        7.76         5.42        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49R TCGA-LN-A49U 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-A4A6 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-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-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        8.78        14.01         5.29         4.80         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        4.44        18.31        36.72         9.17        15.91        18.12 

  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 
                          3.600                           8.085 
[1] "0.0 - 83.2 (3.6)"  "0.1 - 122.1 (8.1)"
[1] "hr=" "1.6"
D56V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(10P11.21) MUTATED         1        0        1        0        14
  DEL PEAK 25(10P11.21) WILD-TYPE       7        4        5        1        21
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10P11.21) MUTATED           6         6          4          3
  DEL PEAK 25(10P11.21) WILD-TYPE        20        17          7          5
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 25(10P11.21) MUTATED            0        1         0
  DEL PEAK 25(10P11.21) WILD-TYPE          6        2         2
D56V3, multiclass
            clus
vv           DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  STAGE I                                1                               7
  STAGE IA                               0                               4
  STAGE IB                               1                               5
  STAGE II                               0                               1
  STAGE IIA                             14                              21
  STAGE IIB                              6                              20
  STAGE III                              6                              17
  STAGE IIIA                             4                               7
  STAGE IIIB                             3                               5
  STAGE IIIC                             0                               6
  STAGE IV                               1                               2
  STAGE IVA                              0                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 25(10P11.21) MUTATED       2 10 23  1
  DEL PEAK 25(10P11.21) WILD-TYPE    24 23 51  3
D56V4, multiclass
       clus
vv      DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  T0+T1                             2                              24
  T2                               10                              23
  T3                               23                              51
  T4                                1                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 25(10P11.21) MUTATED   19 12  4  0
  DEL PEAK 25(10P11.21) WILD-TYPE 45 42  7  6
D56V5, multiclass
    clus
vv   DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  N0                            19                              45
  N1                            12                              42
  N2                             4                               7
  N3                             0                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  DEL PEAK 25(10P11.21) MUTATED   33  0   1  1
  DEL PEAK 25(10P11.21) WILD-TYPE 78  2   2 16
D56V6, multiclass
     clus
vv    DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  M0                             33                              78
  M1                              0                               2
  M1A                             1                               2
  MX                              1                              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10P11.21) MUTATED    5 32
  DEL PEAK 25(10P11.21) WILD-TYPE 16 97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED      5   32
  DEL PEAK 25(10P11.21) WILD-TYPE   16   97
        clus
vv       DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  FEMALE                             5                              16
  MALE                              32                              97
[1] 2 2
[1] FALSE
D56V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10P11.21) MUTATED      16                         1    17
  DEL PEAK 25(10P11.21) WILD-TYPE    22                         1    76
D56V9, multiclass
                           clus
vv                          DEL PEAK 25(10P11.21) MUTATED
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                17
                           clus
vv                          DEL PEAK 25(10P11.21) WILD-TYPE
  ASIAN                                                  22
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK 26(10Q21.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(10Q21.1) MUTATED   23  9
  DEL PEAK 26(10Q21.1) WILD-TYPE 65 45
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            32                            110 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                             9                             45 
$`DEL PEAK 26(10Q21.1) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5S3 
       14.30        13.94        33.27         0.85         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OE 
        0.43        68.02        23.18         3.16         0.30         3.52 
TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A8NK 
        3.35         6.41         1.38         3.16         4.90        13.55 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 
       27.12        83.24         0.10         0.07         0.13         0.10 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6Y0 
        0.10         0.10         0.07         0.20         1.18        53.95 
TCGA-V5-A7RC TCGA-V5-A7RE 
        3.42         4.80 

$`DEL PEAK 26(10Q21.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
       16.24         4.21        32.45        20.09        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         0.03         0.26         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        14.86         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39         3.68        41.52        42.77        25.41        15.48 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J 
       25.28        18.08        17.59         6.21         3.45         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        8.94         3.68        19.50         8.78         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         7.17        30.74        29.00         7.13         7.43 
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-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45         0.16         0.07         0.33         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 
        0.10         0.07         0.10         0.07         0.10         0.07 
TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07        17.62         5.16         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 TCGA-V5-AASV TCGA-V5-AASW 
        7.00         8.78        14.01         5.29         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        4.44        18.31         8.12        36.72        12.03         9.17 
TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.91        18.12 

  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                         3.255                          8.315 
[1] "0.1 - 83.2 (3.3)"  "0.0 - 122.1 (8.3)"
[1] "hr=" "1.2"
D57V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(10Q21.1) MUTATED         2        1        1        1        13
  DEL PEAK 26(10Q21.1) WILD-TYPE       6        3        5        0        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10Q21.1) MUTATED           4         5          3          2
  DEL PEAK 26(10Q21.1) WILD-TYPE        22        18          8          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 26(10Q21.1) MUTATED            0        1         0
  DEL PEAK 26(10Q21.1) WILD-TYPE          6        2         2
D57V3, multiclass
            clus
vv           DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  STAGE I                               2                              6
  STAGE IA                              1                              3
  STAGE IB                              1                              5
  STAGE II                              1                              0
  STAGE IIA                            13                             22
  STAGE IIB                             4                             22
  STAGE III                             5                             18
  STAGE IIIA                            3                              8
  STAGE IIIB                            2                              6
  STAGE IIIC                            0                              6
  STAGE IV                              1                              2
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 26(10Q21.1) MUTATED       5  9 18  1
  DEL PEAK 26(10Q21.1) WILD-TYPE    21 24 56  3
D57V4, multiclass
       clus
vv      DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  T0+T1                            5                             21
  T2                               9                             24
  T3                              18                             56
  T4                               1                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 26(10Q21.1) MUTATED   20  9  3  0
  DEL PEAK 26(10Q21.1) WILD-TYPE 44 45  8  6
D57V5, multiclass
    clus
vv   DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  N0                           20                             44
  N1                            9                             45
  N2                            3                              8
  N3                            0                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 26(10Q21.1) MUTATED   29  0   1  2
  DEL PEAK 26(10Q21.1) WILD-TYPE 82  2   2 15
D57V6, multiclass
     clus
vv    DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  M0                            29                             82
  M1                             0                              2
  M1A                            1                              2
  MX                             2                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(10Q21.1) MUTATED    6 30
  DEL PEAK 26(10Q21.1) WILD-TYPE 15 99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q21.1) MUTATED      6   30
  DEL PEAK 26(10Q21.1) WILD-TYPE   15   99
        clus
vv       DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  FEMALE                            6                             15
  MALE                             30                             99
[1] 2 2
[1] FALSE
D57V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(10Q21.1) MUTATED      17                         1    16
  DEL PEAK 26(10Q21.1) WILD-TYPE    21                         1    77
D57V9, multiclass
                           clus
vv                          DEL PEAK 26(10Q21.1) MUTATED
  ASIAN                                               17
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               16
                           clus
vv                          DEL PEAK 26(10Q21.1) WILD-TYPE
  ASIAN                                                 21
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 27(10Q23.31) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 27(10Q23.31) MUTATED   30 20
  DEL PEAK 27(10Q23.31) WILD-TYPE 58 34
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             50                              92 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             20                              34 
$`DEL PEAK 27(10Q23.31) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94        16.24         4.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 
       33.27        20.09         0.85         2.63         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
        0.43        44.75        23.18         3.16         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
        8.94         3.52         3.35        19.50         6.41         3.32 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NE TCGA-L5-A8NI 
        3.16        30.74         4.90         7.13        55.50        13.48 
TCGA-L5-A8NK TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       13.55        27.12        83.24        10.45         0.16         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.07         0.13         0.10         0.10         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 
        0.20         1.18         5.16         7.59         5.06        53.95 
TCGA-V5-A7RC TCGA-V5-A7RE 
        3.42         4.80 

$`DEL PEAK 27(10Q23.31) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3YA 
       31.27        58.55         7.63         8.94        32.45        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         0.03         0.26         0.99        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB 
        0.36         0.13        14.86         0.46       122.10        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        15.48 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF 
       25.28        18.08        17.59         6.21         3.45         3.68 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU 
        8.78         4.08        18.35         7.17         1.38        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.95         3.02         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       13.41        52.57        46.09        10.36         0.07         0.07 
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-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.07         0.10         0.07         0.07        17.62         3.78 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        8.02        14.70         7.04        29.59         6.35         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        7.00         8.78        14.01         5.29         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        4.44        18.31         8.12        36.72        12.03         9.17 
TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.91        18.12 

  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 
                          4.980                           8.315 
[1] "0.1 - 83.2 (5.0)"  "0.0 - 122.1 (8.3)"
[1] "hr=" "1.3"
D58V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10Q23.31) MUTATED         3        1        1        1        14
  DEL PEAK 27(10Q23.31) WILD-TYPE       5        3        5        0        21
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10Q23.31) MUTATED          10         9          3          3
  DEL PEAK 27(10Q23.31) WILD-TYPE        16        14          8          5
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 27(10Q23.31) MUTATED            1        1         1
  DEL PEAK 27(10Q23.31) WILD-TYPE          5        2         1
D58V3, multiclass
            clus
vv           DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  STAGE I                                3                               5
  STAGE IA                               1                               3
  STAGE IB                               1                               5
  STAGE II                               1                               0
  STAGE IIA                             14                              21
  STAGE IIB                             10                              16
  STAGE III                              9                              14
  STAGE IIIA                             3                               8
  STAGE IIIB                             3                               5
  STAGE IIIC                             1                               5
  STAGE IV                               1                               2
  STAGE IVA                              1                               1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 27(10Q23.31) MUTATED       6 14 28  1
  DEL PEAK 27(10Q23.31) WILD-TYPE    20 19 46  3
D58V4, multiclass
       clus
vv      DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  T0+T1                             6                              20
  T2                               14                              19
  T3                               28                              46
  T4                                1                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 27(10Q23.31) MUTATED   24 19  4  1
  DEL PEAK 27(10Q23.31) WILD-TYPE 40 35  7  5
D58V5, multiclass
    clus
vv   DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  N0                            24                              40
  N1                            19                              35
  N2                             4                               7
  N3                             1                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  DEL PEAK 27(10Q23.31) MUTATED   43  0   2  3
  DEL PEAK 27(10Q23.31) WILD-TYPE 68  2   1 14
D58V6, multiclass
     clus
vv    DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  M0                             43                              68
  M1                              0                               2
  M1A                             2                               1
  MX                              3                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                 cls
clus                               0  1
  DEL PEAK 27(10Q23.31) MUTATED   10 44
  DEL PEAK 27(10Q23.31) WILD-TYPE 11 85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED     10   44
  DEL PEAK 27(10Q23.31) WILD-TYPE   11   85
        clus
vv       DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  FEMALE                            10                              11
  MALE                              44                              85
[1] 2 2
[1] FALSE
D58V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(10Q23.31) MUTATED      19                         1    26
  DEL PEAK 27(10Q23.31) WILD-TYPE    19                         1    67
D58V9, multiclass
                           clus
vv                          DEL PEAK 27(10Q23.31) MUTATED
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                26
                           clus
vv                          DEL PEAK 27(10Q23.31) WILD-TYPE
  ASIAN                                                  19
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = DEL PEAK 28(11P15.4) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(11P15.4) MUTATED   42 15
  DEL PEAK 28(11P15.4) WILD-TYPE 46 39
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            57                             85 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            15                             39 
$`DEL PEAK 28(11P15.4) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3Y9 
       31.27        14.30         5.92         4.21        32.45         0.85 
TCGA-IG-A3YB TCGA-IG-A50L TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H 
        2.63         0.53        25.41        18.08         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO 
        4.31         8.94         3.68         3.35        19.50         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
        7.17         1.38         3.16         6.94         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.95         3.02        55.50        16.47        13.55        13.22 
TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       13.41        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-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
       29.59        53.95         8.78         3.42         4.80         8.15 
TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA7I 
        4.44         8.12        15.91 

$`DEL PEAK 28(11P15.4) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        58.55         7.63        13.94         8.94        16.24 
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-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.99        17.03         0.79        23.41         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         0.46         0.43       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        42.77        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OI 
       25.28        17.59         6.21         3.45         3.52         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        6.41         4.08        18.35        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NF 
        7.13         7.43         8.71        25.12         7.40         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       35.97        12.92        13.48         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49V 
        8.71        27.12        83.24        52.57        46.09         0.10 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.07         0.10         0.10         0.07         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       17.62         5.16         3.78         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW 
       14.70         7.04         6.35         9.30         7.00        14.01 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        5.29         8.48        18.31        36.72        12.03         9.17 
TCGA-ZR-A9CJ 
       18.12 

  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 
                          55.5                          122.1 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                          3.68                           8.94 
[1] "0.1 - 55.5 (3.7)"  "0.0 - 122.1 (8.9)"
[1] "hr=" "1"  
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(11P15.4) MUTATED         3        2        2        1        15
  DEL PEAK 28(11P15.4) WILD-TYPE       5        2        4        0        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(11P15.4) MUTATED           8        12          6          1
  DEL PEAK 28(11P15.4) WILD-TYPE        18        11          5          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 28(11P15.4) MUTATED            2        0         0
  DEL PEAK 28(11P15.4) WILD-TYPE          4        3         2
D59V3, multiclass
            clus
vv           DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              2                              2
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            15                             20
  STAGE IIB                             8                             18
  STAGE III                            12                             11
  STAGE IIIA                            6                              5
  STAGE IIIB                            1                              7
  STAGE IIIC                            2                              4
  STAGE IV                              0                              3
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 28(11P15.4) MUTATED       9 10 34  2
  DEL PEAK 28(11P15.4) WILD-TYPE    17 23 40  2
D59V4, multiclass
       clus
vv      DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  T0+T1                            9                             17
  T2                              10                             23
  T3                              34                             40
  T4                               2                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 28(11P15.4) MUTATED   29 21  3  2
  DEL PEAK 28(11P15.4) WILD-TYPE 35 33  8  4
D59V5, multiclass
    clus
vv   DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  N0                           29                             35
  N1                           21                             33
  N2                            3                              8
  N3                            2                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 28(11P15.4) MUTATED   44  0   0 10
  DEL PEAK 28(11P15.4) WILD-TYPE 67  2   3  7
D59V6, multiclass
     clus
vv    DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  M0                            44                             67
  M1                             0                              2
  M1A                            0                              3
  MX                            10                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED    5 56
  DEL PEAK 28(11P15.4) WILD-TYPE 16 73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED      5   56
  DEL PEAK 28(11P15.4) WILD-TYPE   16   73
        clus
vv       DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  FEMALE                            5                             16
  MALE                             56                             73
[1] 2 2
[1] FALSE
D59V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(11P15.4) MUTATED      22                         1    32
  DEL PEAK 28(11P15.4) WILD-TYPE    16                         1    61
D59V9, multiclass
                           clus
vv                          DEL PEAK 28(11P15.4) MUTATED
  ASIAN                                               22
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               32
                           clus
vv                          DEL PEAK 28(11P15.4) WILD-TYPE
  ASIAN                                                 16
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 29(11Q25) MUTATION ANALYSIS
D60V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 29(11Q25) MUTATED   36 23
  DEL PEAK 29(11Q25) WILD-TYPE 52 31
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          59                           83 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          23                           31 
$`DEL PEAK 29(11Q25) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       14.30         7.63         5.92        20.12         0.03         0.26 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FH TCGA-L5-A43C 
       17.03        23.41         0.13         0.43        42.77         3.16 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
        0.30         3.68         4.08         3.32         7.17         3.16 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       29.00         6.94         2.60         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NT TCGA-L5-A8NV 
        2.66        12.92        13.55        13.22        27.12        52.57 
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-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-S8-A6BV 
        3.78         8.02         7.59         5.06         6.35         8.78 
TCGA-V5-A7RC TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA7D TCGA-VR-AA7I 
        3.42        18.31         8.12         9.17        15.91 

$`DEL PEAK 29(11Q25) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP 
        2.63         0.99         0.53         0.79         0.36        14.86 
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        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        25.41        15.48        23.18        25.28        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       17.59         6.21         3.45         4.31         8.94         3.52 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
        3.35        19.50         8.78         6.41        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
       30.74         4.90         7.13         7.43         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM 
        0.36         7.40        35.97        13.48        16.47         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.42        21.37         8.71        13.41        83.24        46.09 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 
        0.33         0.13         0.07         0.10         0.07         0.10 
TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        0.07        17.62        14.70         7.04        29.59        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        9.30         7.00        14.01         5.29         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-ZR-A9CJ 
        8.15         4.44        36.72        12.03        18.12 

  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                        0.03                         0.07 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                        55.5                        122.1 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                        3.95                         8.94 
[1] "0.0 - 55.5 (4.0)"  "0.1 - 122.1 (8.9)"
[1] "hr=" "1.9"
D60V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(11Q25) MUTATED         1        3        1        1        17
  DEL PEAK 29(11Q25) WILD-TYPE       7        1        5        0        18
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(11Q25) MUTATED          10        11          2          4
  DEL PEAK 29(11Q25) WILD-TYPE        16        12          9          4
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 29(11Q25) MUTATED            3        2         1
  DEL PEAK 29(11Q25) WILD-TYPE          3        1         1
D60V3, multiclass
            clus
vv           DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  STAGE I                             1                            7
  STAGE IA                            3                            1
  STAGE IB                            1                            5
  STAGE II                            1                            0
  STAGE IIA                          17                           18
  STAGE IIB                          10                           16
  STAGE III                          11                           12
  STAGE IIIA                          2                            9
  STAGE IIIB                          4                            4
  STAGE IIIC                          3                            3
  STAGE IV                            2                            1
  STAGE IVA                           1                            1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 29(11Q25) MUTATED       9 16 31  1
  DEL PEAK 29(11Q25) WILD-TYPE    17 17 43  3
D60V4, multiclass
       clus
vv      DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  T0+T1                          9                           17
  T2                            16                           17
  T3                            31                           43
  T4                             1                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 29(11Q25) MUTATED   27 22  4  3
  DEL PEAK 29(11Q25) WILD-TYPE 37 32  7  3
D60V5, multiclass
    clus
vv   DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  N0                         27                           37
  N1                         22                           32
  N2                          4                            7
  N3                          3                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 M1A MX
  DEL PEAK 29(11Q25) MUTATED   46  2   1  6
  DEL PEAK 29(11Q25) WILD-TYPE 65  0   2 11
D60V6, multiclass
     clus
vv    DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  M0                          46                           65
  M1                           2                            0
  M1A                          1                            2
  MX                           6                           11
[1] 4 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 29(11Q25) MUTATED    7 56
  DEL PEAK 29(11Q25) WILD-TYPE 14 73
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(11Q25) MUTATED      7   56
  DEL PEAK 29(11Q25) WILD-TYPE   14   73
        clus
vv       DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  FEMALE                          7                           14
  MALE                           56                           73
[1] 2 2
[1] FALSE
D60V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(11Q25) MUTATED      21                         1    37
  DEL PEAK 29(11Q25) WILD-TYPE    17                         1    56
D60V9, multiclass
                           clus
vv                          DEL PEAK 29(11Q25) MUTATED
  ASIAN                                             21
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             37
                           clus
vv                          DEL PEAK 29(11Q25) WILD-TYPE
  ASIAN                                               17
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 30(12Q23.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(12Q23.1) MUTATED   28 13
  DEL PEAK 30(12Q23.1) WILD-TYPE 60 41
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            41                            101 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            13                             41 
$`DEL PEAK 30(12Q23.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78        31.27        14.30        13.94        32.45        33.27 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FD 
        2.63         0.03         0.79        23.41         0.43        68.02 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OH 
       42.77        25.41        18.08         3.45         8.94        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88V 
        6.41         3.32         7.17        30.74         7.13         2.60 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NS TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A5U6 TCGA-Q9-A6FW TCGA-R6-A6KZ 
       13.41         0.16         0.33         0.20         3.78         5.06 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-A8Q7 
        8.78        14.01         3.42         4.44        36.72 

$`DEL PEAK 30(12Q23.1) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92         8.94        16.24         4.21 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09         0.85        20.78        20.12         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03         0.36         0.13        14.86         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        60.39         3.68        41.52        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       23.18        25.28        17.59         6.21         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM 
        4.31         3.52         3.68         3.35         8.78         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
       18.35         1.38         3.16         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG 
        6.94         8.71        25.12         7.40         3.95        35.97 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.07        10.45         0.07         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-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-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EU 
        7.00         5.29         4.80         8.48         8.15        18.31 
TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.12        12.03         9.17        15.91        18.12 

  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                         68.02                         122.10 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                          8.78                           7.43 
[1] "0.0 - 68.0 (8.8)"  "0.1 - 122.1 (7.4)"
[1] "hr=" "1.4"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(12Q23.1) MUTATED         4        1        2        0         7
  DEL PEAK 30(12Q23.1) WILD-TYPE       4        3        4        1        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(12Q23.1) MUTATED          11         4          4          1
  DEL PEAK 30(12Q23.1) WILD-TYPE        15        19          7          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 30(12Q23.1) MUTATED            1        1         1
  DEL PEAK 30(12Q23.1) WILD-TYPE          5        2         1
D61V3, multiclass
            clus
vv           DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              3
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                             7                             28
  STAGE IIB                            11                             15
  STAGE III                             4                             19
  STAGE IIIA                            4                              7
  STAGE IIIB                            1                              7
  STAGE IIIC                            1                              5
  STAGE IV                              1                              2
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 30(12Q23.1) MUTATED      10  8 21  0
  DEL PEAK 30(12Q23.1) WILD-TYPE    16 25 53  4
D61V4, multiclass
       clus
vv      DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  T0+T1                           10                             16
  T2                               8                             25
  T3                              21                             53
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 30(12Q23.1) MUTATED   19 16  2  1
  DEL PEAK 30(12Q23.1) WILD-TYPE 45 38  9  5
D61V5, multiclass
    clus
vv   DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  N0                           19                             45
  N1                           16                             38
  N2                            2                              9
  N3                            1                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 30(12Q23.1) MUTATED   31  1   1  6
  DEL PEAK 30(12Q23.1) WILD-TYPE 80  1   2 11
D61V6, multiclass
     clus
vv    DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  M0                            31                             80
  M1                             1                              1
  M1A                            1                              2
  MX                             6                             11
[1] 4 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 30(12Q23.1) MUTATED    9 33
  DEL PEAK 30(12Q23.1) WILD-TYPE 12 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q23.1) MUTATED      9   33
  DEL PEAK 30(12Q23.1) WILD-TYPE   12   96
        clus
vv       DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  FEMALE                            9                             12
  MALE                             33                             96
[1] 2 2
[1] FALSE
D61V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(12Q23.1) MUTATED       6                         1    28
  DEL PEAK 30(12Q23.1) WILD-TYPE    32                         1    65
D61V9, multiclass
                           clus
vv                          DEL PEAK 30(12Q23.1) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               28
                           clus
vv                          DEL PEAK 30(12Q23.1) WILD-TYPE
  ASIAN                                                 32
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = DEL PEAK 31(13Q12.11) MUTATION ANALYSIS
D62V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 31(13Q12.11) MUTATED   36 20
  DEL PEAK 31(13Q12.11) WILD-TYPE 52 34
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             56                              86 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             20                              34 
$`DEL PEAK 31(13Q12.11) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3QL 
       25.78        58.55         7.63         8.94        32.45        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 
        0.85        20.78         2.63         0.26        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A93C 
       23.41         0.13         0.46        60.39        68.02        23.18 
TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OT 
       18.08         8.94         3.68         4.08         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NW 
       29.00         6.94        13.22         5.42        83.24        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         0.07        10.45         0.16         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-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-Q9-A6FU 
        0.10         0.10         0.10         0.07         0.20         5.16 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EU 
        5.06        29.59         6.35         4.80         8.48        18.31 
TCGA-VR-A8Q7 TCGA-VR-AA7I 
       36.72        15.91 

$`DEL PEAK 31(13Q12.11) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-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-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         0.43       122.10        44.75         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        25.41        15.48        25.28        17.59         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
        3.16         3.45         0.30         4.31         3.52         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.50         8.78         6.41        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        1.38        30.74         7.13         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
        7.76        21.37         8.71        13.41        27.12        52.57 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
        1.18        17.62         3.78         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        7.04        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA4G 
        5.29         3.42         8.15         4.44         8.12        12.03 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

  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 
                           5.29                            8.07 
[1] "0.1 - 83.2 (5.3)"  "0.0 - 122.1 (8.1)"
[1] "hr=" "1.1"
D62V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(13Q12.11) MUTATED         2        2        4        1        15
  DEL PEAK 31(13Q12.11) WILD-TYPE       6        2        2        0        20
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(13Q12.11) MUTATED           8        11          5          4
  DEL PEAK 31(13Q12.11) WILD-TYPE        18        12          6          4
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 31(13Q12.11) MUTATED            1        2         0
  DEL PEAK 31(13Q12.11) WILD-TYPE          5        1         2
D62V3, multiclass
            clus
vv           DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  STAGE I                                2                               6
  STAGE IA                               2                               2
  STAGE IB                               4                               2
  STAGE II                               1                               0
  STAGE IIA                             15                              20
  STAGE IIB                              8                              18
  STAGE III                             11                              12
  STAGE IIIA                             5                               6
  STAGE IIIB                             4                               4
  STAGE IIIC                             1                               5
  STAGE IV                               2                               1
  STAGE IVA                              0                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 31(13Q12.11) MUTATED       8 12 33  3
  DEL PEAK 31(13Q12.11) WILD-TYPE    18 21 41  1
D62V4, multiclass
       clus
vv      DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  T0+T1                             8                              18
  T2                               12                              21
  T3                               33                              41
  T4                                3                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 31(13Q12.11) MUTATED   29 21  5  1
  DEL PEAK 31(13Q12.11) WILD-TYPE 35 33  6  5
D62V5, multiclass
    clus
vv   DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  N0                            29                              35
  N1                            21                              33
  N2                             5                               6
  N3                             1                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  DEL PEAK 31(13Q12.11) MUTATED   47  1   1  5
  DEL PEAK 31(13Q12.11) WILD-TYPE 64  1   2 12
D62V6, multiclass
     clus
vv    DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  M0                             47                              64
  M1                              1                               1
  M1A                             1                               2
  MX                              5                              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED    5 54
  DEL PEAK 31(13Q12.11) WILD-TYPE 16 75
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED      5   54
  DEL PEAK 31(13Q12.11) WILD-TYPE   16   75
        clus
vv       DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  FEMALE                             5                              16
  MALE                              54                              75
[1] 2 2
[1] FALSE
D62V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(13Q12.11) MUTATED      22                         1    30
  DEL PEAK 31(13Q12.11) WILD-TYPE    16                         1    63
D62V9, multiclass
                           clus
vv                          DEL PEAK 31(13Q12.11) MUTATED
  ASIAN                                                22
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                30
                           clus
vv                          DEL PEAK 31(13Q12.11) WILD-TYPE
  ASIAN                                                  16
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 32(13Q14.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 32(13Q14.2) MUTATED   38 19
  DEL PEAK 32(13Q14.2) WILD-TYPE 50 35
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            57                             85 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            19                             35 
$`DEL PEAK 32(13Q14.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A3QL TCGA-IG-A3Y9 
       25.78        58.55         7.63         8.94        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.78         2.63         0.26         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93E 
        0.13        44.75        60.39        68.02         3.68        18.08 
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-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU 
        3.95         3.02        13.48        13.22         5.42        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         0.07        10.45         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-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-A4MR TCGA-LN-A5U6 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-V5-A7RE 
        0.07         0.20         5.06        29.59         6.35         4.80 
TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA7I 
       18.31        36.72        15.91 

$`DEL PEAK 32(13Q14.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
       32.45        33.27        20.12         0.03         0.99         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FG 
        0.36        14.86         0.46         0.43       122.10        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        15.48        23.18        25.28        17.59 
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-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE 
        8.71         2.60        25.12         0.36         7.40        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        35.97        12.92        16.47        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49X 
       21.37         8.71        13.41        27.12        52.57         0.10 
TCGA-LN-A49Y TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.07         0.10         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        3.78         8.02         7.59        14.70         7.04        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30         7.00         8.78        14.01         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D 
        8.48         8.15         4.44         8.12        12.03         9.17 
TCGA-ZR-A9CJ 
       18.12 

  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 
                          4.08                           8.48 
[1] "0.1 - 83.2 (4.1)"  "0.0 - 122.1 (8.5)"
[1] "hr=" "1.1"
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(13Q14.2) MUTATED         4        2        2        1        16
  DEL PEAK 32(13Q14.2) WILD-TYPE       4        2        4        0        19
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(13Q14.2) MUTATED           8        13          6          2
  DEL PEAK 32(13Q14.2) WILD-TYPE        18        10          5          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 32(13Q14.2) MUTATED            1        1         0
  DEL PEAK 32(13Q14.2) WILD-TYPE          5        2         2
D63V3, multiclass
            clus
vv           DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              2
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            16                             19
  STAGE IIB                             8                             18
  STAGE III                            13                             10
  STAGE IIIA                            6                              5
  STAGE IIIB                            2                              6
  STAGE IIIC                            1                              5
  STAGE IV                              1                              2
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 32(13Q14.2) MUTATED      10 14 30  3
  DEL PEAK 32(13Q14.2) WILD-TYPE    16 19 44  1
D63V4, multiclass
       clus
vv      DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  T0+T1                           10                             16
  T2                              14                             19
  T3                              30                             44
  T4                               3                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 32(13Q14.2) MUTATED   29 25  2  1
  DEL PEAK 32(13Q14.2) WILD-TYPE 35 29  9  5
D63V5, multiclass
    clus
vv   DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  N0                           29                             35
  N1                           25                             29
  N2                            2                              9
  N3                            1                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 32(13Q14.2) MUTATED   51  1   0  2
  DEL PEAK 32(13Q14.2) WILD-TYPE 60  1   3 15
D63V6, multiclass
     clus
vv    DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  M0                            51                             60
  M1                             1                              1
  M1A                            0                              3
  MX                             2                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED    5 55
  DEL PEAK 32(13Q14.2) WILD-TYPE 16 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED      5   55
  DEL PEAK 32(13Q14.2) WILD-TYPE   16   74
        clus
vv       DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  FEMALE                            5                             16
  MALE                             55                             74
[1] 2 2
[1] FALSE
D63V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(13Q14.2) MUTATED      24                         0    32
  DEL PEAK 32(13Q14.2) WILD-TYPE    14                         2    61
D63V9, multiclass
                           clus
vv                          DEL PEAK 32(13Q14.2) MUTATED
  ASIAN                                               24
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               32
                           clus
vv                          DEL PEAK 32(13Q14.2) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = DEL PEAK 33(13Q21.31) MUTATION ANALYSIS
D64V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 33(13Q21.31) MUTATED   33 20
  DEL PEAK 33(13Q21.31) WILD-TYPE 55 34
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             53                              89 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             20                              34 
$`DEL PEAK 33(13Q21.31) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 
       58.55         7.63         8.94        32.45        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.78         2.63         0.26         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A4OE 
        0.13        44.75        60.39        68.02        18.08         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-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.48        13.22         5.42        83.24        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        0.07        10.45         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
        0.07         0.07         0.07         0.13         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ 
        0.10         0.07         0.20         7.59         5.06         6.35 
TCGA-R6-A6Y2 TCGA-V5-A7RE TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA7I 
        9.30         4.80        18.31        36.72        15.91 

$`DEL PEAK 33(13Q21.31) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       25.78        31.27        14.30         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
        4.21        33.27        20.12         0.03         0.99         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE 
        0.36        14.86         0.46         0.43       122.10         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       17.59         6.21         3.16         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO 
        8.94         3.35        19.50         8.78        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        30.74         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        6.94         8.71        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.02        55.50         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.55         7.76        21.37         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A8 
       52.57         0.16         0.10         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.10         1.18        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-RE-A7BO 
        8.02        14.70         7.04        29.59        53.95         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        8.78        14.01         5.29         3.42         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
        4.44         8.12        12.03         9.17        18.12 

  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                          83.24                          122.10 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                           5.42                            8.12 
[1] "0.1 - 83.2 (5.4)"  "0.0 - 122.1 (8.1)"
[1] "hr=" "1"  
D64V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(13Q21.31) MUTATED         3        2        2        1        15
  DEL PEAK 33(13Q21.31) WILD-TYPE       5        2        4        0        20
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(13Q21.31) MUTATED           8        11          6          2
  DEL PEAK 33(13Q21.31) WILD-TYPE        18        12          5          6
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 33(13Q21.31) MUTATED            1        1         0
  DEL PEAK 33(13Q21.31) WILD-TYPE          5        2         2
D64V3, multiclass
            clus
vv           DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  STAGE I                                3                               5
  STAGE IA                               2                               2
  STAGE IB                               2                               4
  STAGE II                               1                               0
  STAGE IIA                             15                              20
  STAGE IIB                              8                              18
  STAGE III                             11                              12
  STAGE IIIA                             6                               5
  STAGE IIIB                             2                               6
  STAGE IIIC                             1                               5
  STAGE IV                               1                               2
  STAGE IVA                              0                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 33(13Q21.31) MUTATED       9 12 28  3
  DEL PEAK 33(13Q21.31) WILD-TYPE    17 21 46  1
D64V4, multiclass
       clus
vv      DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  T0+T1                             9                              17
  T2                               12                              21
  T3                               28                              46
  T4                                3                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 33(13Q21.31) MUTATED   27 22  2  1
  DEL PEAK 33(13Q21.31) WILD-TYPE 37 32  9  5
D64V5, multiclass
    clus
vv   DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  N0                            27                              37
  N1                            22                              32
  N2                             2                               9
  N3                             1                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  DEL PEAK 33(13Q21.31) MUTATED   45  1   0  3
  DEL PEAK 33(13Q21.31) WILD-TYPE 66  1   3 14
D64V6, multiclass
     clus
vv    DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  M0                             45                              66
  M1                              1                               1
  M1A                             0                               3
  MX                              3                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                                 cls
clus                               0  1
  DEL PEAK 33(13Q21.31) MUTATED    5 51
  DEL PEAK 33(13Q21.31) WILD-TYPE 16 78
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q21.31) MUTATED      5   51
  DEL PEAK 33(13Q21.31) WILD-TYPE   16   78
        clus
vv       DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  FEMALE                             5                              16
  MALE                              51                              78
[1] 2 2
[1] FALSE
D64V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q21.31) MUTATED      21                         0    31
  DEL PEAK 33(13Q21.31) WILD-TYPE    17                         2    62
D64V9, multiclass
                           clus
vv                          DEL PEAK 33(13Q21.31) MUTATED
  ASIAN                                                21
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                31
                           clus
vv                          DEL PEAK 33(13Q21.31) WILD-TYPE
  ASIAN                                                  17
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = DEL PEAK 34(14Q23.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 34(14Q23.3) MUTATED   24 17
  DEL PEAK 34(14Q23.3) WILD-TYPE 64 37
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            41                            101 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            17                             37 
$`DEL PEAK 34(14Q23.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL 
       31.27         7.63         8.94        16.24         4.21        20.09 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB 
       23.41         0.36         0.46         0.43       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        18.08         0.30         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        3.35         3.16        29.00         7.13         6.94         0.36 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L 
        3.95        55.50         2.66        16.47        10.36        10.45 
TCGA-LN-A49W TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 
        0.07        17.62         7.59         5.06         6.35         9.30 
TCGA-RE-A7BO TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-ZR-A9CJ 
        7.00        18.31        36.72        12.03        18.12 

$`DEL PEAK 34(14Q23.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR 
       25.78        14.30        58.55         5.92        13.94        32.45 
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-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.26         0.99         0.53        17.03         0.79         0.13 
TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       14.86        44.75        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        23.18        25.28        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.45         4.31        19.50         8.78         6.41         4.08 
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-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        7.43         8.71         2.60        25.12         7.40         3.02 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        5.42        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09         0.07         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
        0.10         0.13         0.07         0.10         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-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        3.78         8.02        14.70         7.04        29.59        53.95 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        8.78        14.01         5.29         3.42         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA7D TCGA-VR-AA7I 
        8.15         4.44         8.12         9.17        15.91 

  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                          8.94                           7.17 
[1] "0.1 - 122.1 (8.9)" "0.0 - 83.2 (7.2)" 
[1] "hr=" "1"  
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(14Q23.3) MUTATED         3        1        1        0         6
  DEL PEAK 34(14Q23.3) WILD-TYPE       5        3        5        1        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(14Q23.3) MUTATED           8         7          3          3
  DEL PEAK 34(14Q23.3) WILD-TYPE        18        16          8          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 34(14Q23.3) MUTATED            2        1         2
  DEL PEAK 34(14Q23.3) WILD-TYPE          4        2         0
D65V3, multiclass
            clus
vv           DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              1                              3
  STAGE IB                              1                              5
  STAGE II                              0                              1
  STAGE IIA                             6                             29
  STAGE IIB                             8                             18
  STAGE III                             7                             16
  STAGE IIIA                            3                              8
  STAGE IIIB                            3                              5
  STAGE IIIC                            2                              4
  STAGE IV                              1                              2
  STAGE IVA                             2                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 34(14Q23.3) MUTATED      10  6 24  0
  DEL PEAK 34(14Q23.3) WILD-TYPE    16 27 50  4
D65V4, multiclass
       clus
vv      DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  T0+T1                           10                             16
  T2                               6                             27
  T3                              24                             50
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 34(14Q23.3) MUTATED   14 18  5  2
  DEL PEAK 34(14Q23.3) WILD-TYPE 50 36  6  4
D65V5, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  N0                           14                             50
  N1                           18                             36
  N2                            5                              6
  N3                            2                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 34(14Q23.3) MUTATED   29  1   2  6
  DEL PEAK 34(14Q23.3) WILD-TYPE 82  1   1 11
D65V6, multiclass
     clus
vv    DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  M0                            29                             82
  M1                             1                              1
  M1A                            2                              1
  MX                             6                             11
[1] 4 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 34(14Q23.3) MUTATED    7 37
  DEL PEAK 34(14Q23.3) WILD-TYPE 14 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED      7   37
  DEL PEAK 34(14Q23.3) WILD-TYPE   14   92
        clus
vv       DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  FEMALE                            7                             14
  MALE                             37                             92
[1] 2 2
[1] FALSE
D65V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(14Q23.3) MUTATED       8                         0    28
  DEL PEAK 34(14Q23.3) WILD-TYPE    30                         2    65
D65V9, multiclass
                           clus
vv                          DEL PEAK 34(14Q23.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               28
                           clus
vv                          DEL PEAK 34(14Q23.3) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = DEL PEAK 35(15Q11.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 35(15Q11.2) MUTATED   30 18
  DEL PEAK 35(15Q11.2) WILD-TYPE 58 36
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            48                             94 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            18                             36 
$`DEL PEAK 35(15Q11.2) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YC 
        7.63         5.92        16.24        32.45        20.09        20.12 
TCGA-IG-A4QS TCGA-IG-A625 TCGA-IG-A97H TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D 
        0.26         0.36         0.43        25.41        23.18        25.28 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
       18.08         0.30         8.94         3.52         3.35        19.50 
TCGA-L5-A4OM TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        4.08         4.90        29.00         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       12.92         5.42         8.71        13.41        27.12        83.24 
TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 
       10.45         0.10         0.10         0.07         0.10         0.20 
TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        1.18         5.16         7.59         5.06        14.70        29.59 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         7.00         8.78        14.01         3.42         4.80 

$`DEL PEAK 35(15Q11.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55        13.94         8.94 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 
        4.21        33.27         0.85        20.78         2.63         0.03 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        0.99         0.53        17.03         0.79        23.41         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         0.46       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        42.77        15.48        17.59         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.16         3.45         4.31         3.68         8.78         6.41 
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-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-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        0.36         7.40         3.95        35.97        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW 
       13.55        13.22         7.76        21.37        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       10.36         0.07         0.16         0.07         0.33         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-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-M9-A5M8 
        0.07         0.10         0.10         0.07         0.07        17.62 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-V5-A7RB 
        3.78         8.02         7.04         6.35        53.95         5.29 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 
        8.48         8.15         4.44        18.31         8.12        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       12.03         9.17        15.91        18.12 

  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 
                         7.610                          7.415 
[1] "0.1 - 83.2 (7.6)"  "0.0 - 122.1 (7.4)"
[1] "hr=" "1"  
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(15Q11.2) MUTATED         3        1        2        0         9
  DEL PEAK 35(15Q11.2) WILD-TYPE       5        3        4        1        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(15Q11.2) MUTATED           7         8          3          5
  DEL PEAK 35(15Q11.2) WILD-TYPE        19        15          8          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 35(15Q11.2) MUTATED            1        2         2
  DEL PEAK 35(15Q11.2) WILD-TYPE          5        1         0
D66V3, multiclass
            clus
vv           DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              1                              3
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                             9                             26
  STAGE IIB                             7                             19
  STAGE III                             8                             15
  STAGE IIIA                            3                              8
  STAGE IIIB                            5                              3
  STAGE IIIC                            1                              5
  STAGE IV                              2                              1
  STAGE IVA                             2                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 35(15Q11.2) MUTATED       8  9 27  0
  DEL PEAK 35(15Q11.2) WILD-TYPE    18 24 47  4
D66V4, multiclass
       clus
vv      DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  T0+T1                            8                             18
  T2                               9                             24
  T3                              27                             47
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 35(15Q11.2) MUTATED   20 16  6  1
  DEL PEAK 35(15Q11.2) WILD-TYPE 44 38  5  5
D66V5, multiclass
    clus
vv   DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  N0                           20                             44
  N1                           16                             38
  N2                            6                              5
  N3                            1                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 35(15Q11.2) MUTATED   35  1   3  3
  DEL PEAK 35(15Q11.2) WILD-TYPE 76  1   0 14
D66V6, multiclass
     clus
vv    DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  M0                            35                             76
  M1                             1                              1
  M1A                            3                              0
  MX                             3                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED    8 42
  DEL PEAK 35(15Q11.2) WILD-TYPE 13 87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED      8   42
  DEL PEAK 35(15Q11.2) WILD-TYPE   13   87
        clus
vv       DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  FEMALE                            8                             13
  MALE                             42                             87
[1] 2 2
[1] FALSE
D66V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(15Q11.2) MUTATED      12                         1    31
  DEL PEAK 35(15Q11.2) WILD-TYPE    26                         1    62
D66V9, multiclass
                           clus
vv                          DEL PEAK 35(15Q11.2) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               31
                           clus
vv                          DEL PEAK 35(15Q11.2) WILD-TYPE
  ASIAN                                                 26
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = DEL PEAK 36(16P13.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 36(16P13.3) MUTATED   27 23
  DEL PEAK 36(16P13.3) WILD-TYPE 61 31
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            50                             92 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            23                             31 
$`DEL PEAK 36(16P13.3) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A3YC TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E 
       32.45        20.12        42.77        25.41        23.18        18.08 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OQ 
        3.16         8.94         3.52         3.35        19.50         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        3.16        30.74         0.36         7.40         3.95         3.02 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
       12.92        13.48         5.42        27.12        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ 
       10.36        10.45         0.07         0.10         0.10         0.10 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.16         8.02         5.06        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        9.30         7.00         5.29         3.42         4.80         8.15 
TCGA-VR-A8Q7 TCGA-VR-AA7I 
       36.72        15.91 

$`DEL PEAK 36(16P13.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL 
       25.78        31.27        14.30        16.24        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         0.46         0.43       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
       68.02         3.68        41.52        15.48        25.28        17.59 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI 
        6.21         3.45         0.30         4.31         3.68         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT 
        6.41         4.08        18.35         3.32         7.17         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NK 
       25.12        55.50         2.66        35.97        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76        21.37         8.71        13.41        83.24 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.07         0.16         0.33         0.10         0.13         0.07 
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-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-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-S8-A6BV 
       17.62         3.78         7.59        14.70         7.04         8.78 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G 
       14.01         8.48         4.44        18.31         8.12        12.03 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                         58.55                         122.10 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                         8.085                          7.150 
[1] "0.1 - 58.5 (8.1)"  "0.0 - 122.1 (7.2)"
[1] "hr=" "1.2"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(16P13.3) MUTATED         4        1        2        0         7
  DEL PEAK 36(16P13.3) WILD-TYPE       4        3        4        1        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(16P13.3) MUTATED           7         9          4          3
  DEL PEAK 36(16P13.3) WILD-TYPE        19        14          7          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 36(16P13.3) MUTATED            1        1         0
  DEL PEAK 36(16P13.3) WILD-TYPE          5        2         2
D67V3, multiclass
            clus
vv           DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              3
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                             7                             28
  STAGE IIB                             7                             19
  STAGE III                             9                             14
  STAGE IIIA                            4                              7
  STAGE IIIB                            3                              5
  STAGE IIIC                            1                              5
  STAGE IV                              1                              2
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 36(16P13.3) MUTATED      12  8 22  1
  DEL PEAK 36(16P13.3) WILD-TYPE    14 25 52  3
D67V4, multiclass
       clus
vv      DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  T0+T1                           12                             14
  T2                               8                             25
  T3                              22                             52
  T4                               1                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 36(16P13.3) MUTATED   17 20  5  1
  DEL PEAK 36(16P13.3) WILD-TYPE 47 34  6  5
D67V5, multiclass
    clus
vv   DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  N0                           17                             47
  N1                           20                             34
  N2                            5                              6
  N3                            1                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 36(16P13.3) MUTATED   35  1   0  6
  DEL PEAK 36(16P13.3) WILD-TYPE 76  1   3 11
D67V6, multiclass
     clus
vv    DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  M0                            35                             76
  M1                             1                              1
  M1A                            0                              3
  MX                             6                             11
[1] 4 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 36(16P13.3) MUTATED    7 45
  DEL PEAK 36(16P13.3) WILD-TYPE 14 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED      7   45
  DEL PEAK 36(16P13.3) WILD-TYPE   14   84
        clus
vv       DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  FEMALE                            7                             14
  MALE                             45                             84
[1] 2 2
[1] FALSE
D67V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(16P13.3) MUTATED       8                         1    34
  DEL PEAK 36(16P13.3) WILD-TYPE    30                         1    59
D67V9, multiclass
                           clus
vv                          DEL PEAK 36(16P13.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               34
                           clus
vv                          DEL PEAK 36(16P13.3) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = DEL PEAK 37(16Q23.1) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 37(16Q23.1) MUTATED   41 25
  DEL PEAK 37(16Q23.1) WILD-TYPE 47 29
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            66                             76 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            25                             29 
$`DEL PEAK 37(16Q23.1) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A97H 
        4.21        20.09        20.12         0.26         0.53         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D 
      122.10        60.39        42.77        25.41        23.18        25.28 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ 
       18.08         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-A8NE 
        7.43         2.60         0.36         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        35.97        16.47        13.22         7.76         5.42 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        83.24        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4MQ TCGA-LN-A4MR 
       10.45         0.33         0.10         0.07         0.10         0.07 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59         5.06        14.70         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-ZR-A9CJ 
        9.30         7.00         5.29         4.80         8.15        18.12 

$`DEL PEAK 37(16Q23.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 
       25.78        14.30        58.55        32.45        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.78         2.63         0.03         0.99        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA 
       23.41         0.36         0.13        14.86         0.46        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC 
       68.02         3.68        41.52        15.48        17.59         6.21 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        3.45         0.30         4.31         3.35        19.50         8.78 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88T 
        4.08         3.32         7.17         1.38         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NQ 
       25.12         7.40        12.92        13.48        13.55        21.37 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S 
       52.57         0.07         0.16         0.07         0.10         0.13 
TCGA-LN-A49U 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-A5U6 TCGA-LN-A5U7 
        0.10         0.10         0.07         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-S8-A6BV 
       17.62         5.16         3.78         7.04        29.59         8.78 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
       14.01         3.42         8.48         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       36.72        12.03         9.17        15.91 

  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                        122.10                          68.02 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                         8.085                          6.575 
[1] "0.1 - 122.1 (8.1)" "0.0 - 68.0 (6.6)" 
[1] "hr=" "1.3"
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(16Q23.1) MUTATED         4        1        2        0        11
  DEL PEAK 37(16Q23.1) WILD-TYPE       4        3        4        1        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(16Q23.1) MUTATED          15        13          3          3
  DEL PEAK 37(16Q23.1) WILD-TYPE        11        10          8          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 37(16Q23.1) MUTATED            3        1         2
  DEL PEAK 37(16Q23.1) WILD-TYPE          3        2         0
D68V3, multiclass
            clus
vv           DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              3
  STAGE IB                              2                              4
  STAGE II                              0                              1
  STAGE IIA                            11                             24
  STAGE IIB                            15                             11
  STAGE III                            13                             10
  STAGE IIIA                            3                              8
  STAGE IIIB                            3                              5
  STAGE IIIC                            3                              3
  STAGE IV                              1                              2
  STAGE IVA                             2                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 37(16Q23.1) MUTATED      14 14 34  0
  DEL PEAK 37(16Q23.1) WILD-TYPE    12 19 40  4
D68V4, multiclass
       clus
vv      DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  T0+T1                           14                             12
  T2                              14                             19
  T3                              34                             40
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 37(16Q23.1) MUTATED   22 32  4  3
  DEL PEAK 37(16Q23.1) WILD-TYPE 42 22  7  3
D68V5, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  N0                           22                             42
  N1                           32                             22
  N2                            4                              7
  N3                            3                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 37(16Q23.1) MUTATED   49  0   3  7
  DEL PEAK 37(16Q23.1) WILD-TYPE 62  2   0 10
D68V6, multiclass
     clus
vv    DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  M0                            49                             62
  M1                             0                              2
  M1A                            3                              0
  MX                             7                             10
[1] 4 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 37(16Q23.1) MUTATED    9 62
  DEL PEAK 37(16Q23.1) WILD-TYPE 12 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      9   62
  DEL PEAK 37(16Q23.1) WILD-TYPE   12   67
        clus
vv       DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  FEMALE                            9                             12
  MALE                             62                             67
[1] 2 2
[1] FALSE
D68V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(16Q23.1) MUTATED      14                         0    46
  DEL PEAK 37(16Q23.1) WILD-TYPE    24                         2    47
D68V9, multiclass
                           clus
vv                          DEL PEAK 37(16Q23.1) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               46
                           clus
vv                          DEL PEAK 37(16Q23.1) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = DEL PEAK 38(17P12) MUTATION ANALYSIS
D69V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 38(17P12) MUTATED   41 25
  DEL PEAK 38(17P12) WILD-TYPE 47 29
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          66                           76 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          25                           29 
$`DEL PEAK 38(17P12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78         7.63         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       32.45         0.03         0.26         0.79        23.41         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93E 
      122.10        60.39        42.77        25.41        25.28        18.08 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO 
        3.45         3.52         3.68         3.35        19.50         3.32 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        7.17         4.90        29.00         7.13         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        0.36         3.95        55.50        35.97        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22         5.42         8.71        13.41        27.12        83.24 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        0.07        10.45         0.16         0.13         0.07         0.07 
TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.20        17.62         5.16         3.78         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        7.04        29.59         9.30         7.00         8.78        14.01 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-ZR-A9CJ 
        4.80         8.15         4.44        18.31         8.12        18.12 

$`DEL PEAK 38(17P12) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL 
       31.27        14.30        58.55        16.24        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L 
        0.85        20.78         2.63        20.12         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA 
       17.03         0.36         0.13        14.86         0.46        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F 
       68.02         3.68        41.52        15.48        23.18        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
        6.21         3.16         0.30         4.31         8.94         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        6.41         4.08        18.35         1.38         3.16        30.74 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
        6.94         8.71        25.12         7.40         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW 
       12.92        13.55         7.76        21.37        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X 
       10.36         0.07         0.33         0.10         0.10         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-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-R6-A6DN 
        0.07         0.07         0.10         0.07         1.18         8.02 
TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       14.70         6.35        53.95         5.29         3.42         8.48 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       36.72        12.03         9.17        15.91 

  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                        0.03                         0.07 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                      122.10                        68.02 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                        7.61                         7.17 
[1] "0.0 - 122.1 (7.6)" "0.1 - 68.0 (7.2)" 
[1] "hr=" "1.1"
D69V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(17P12) MUTATED         5        1        3        0        13
  DEL PEAK 38(17P12) WILD-TYPE       3        3        3        1        22
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(17P12) MUTATED          13        13          2          5
  DEL PEAK 38(17P12) WILD-TYPE        13        10          9          3
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 38(17P12) MUTATED            3        2         0
  DEL PEAK 38(17P12) WILD-TYPE          3        1         2
D69V3, multiclass
            clus
vv           DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  STAGE I                             5                            3
  STAGE IA                            1                            3
  STAGE IB                            3                            3
  STAGE II                            0                            1
  STAGE IIA                          13                           22
  STAGE IIB                          13                           13
  STAGE III                          13                           10
  STAGE IIIA                          2                            9
  STAGE IIIB                          5                            3
  STAGE IIIC                          3                            3
  STAGE IV                            2                            1
  STAGE IVA                           0                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 38(17P12) MUTATED      12 13 37  0
  DEL PEAK 38(17P12) WILD-TYPE    14 20 37  4
D69V4, multiclass
       clus
vv      DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  T0+T1                         12                           14
  T2                            13                           20
  T3                            37                           37
  T4                             0                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 38(17P12) MUTATED   26 27  5  3
  DEL PEAK 38(17P12) WILD-TYPE 38 27  6  3
D69V5, multiclass
    clus
vv   DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  N0                         26                           38
  N1                         27                           27
  N2                          5                            6
  N3                          3                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 M1A MX
  DEL PEAK 38(17P12) MUTATED   52  1   1  6
  DEL PEAK 38(17P12) WILD-TYPE 59  1   2 11
D69V6, multiclass
     clus
vv    DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  M0                          52                           59
  M1                           1                            1
  M1A                          1                            2
  MX                           6                           11
[1] 4 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 38(17P12) MUTATED    8 61
  DEL PEAK 38(17P12) WILD-TYPE 13 68
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED      8   61
  DEL PEAK 38(17P12) WILD-TYPE   13   68
        clus
vv       DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  FEMALE                          8                           13
  MALE                           61                           68
[1] 2 2
[1] FALSE
D69V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(17P12) MUTATED      12                         0    47
  DEL PEAK 38(17P12) WILD-TYPE    26                         2    46
D69V9, multiclass
                           clus
vv                          DEL PEAK 38(17P12) MUTATED
  ASIAN                                             12
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             47
                           clus
vv                          DEL PEAK 38(17P12) WILD-TYPE
  ASIAN                                               26
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = DEL PEAK 39(17Q25.3) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 39(17Q25.3) MUTATED   25  6
  DEL PEAK 39(17Q25.3) WILD-TYPE 63 48
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                            31                            111 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                             6                             48 
$`DEL PEAK 39(17Q25.3) MUTATED`
TCGA-2H-A9GN TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A938 
        8.94         0.03         0.79        23.41         0.43        25.41 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88Y 
        3.35        19.50         6.41         3.16        29.00         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NR TCGA-LN-A49M 
        7.40         3.95        55.50        35.97         8.71         0.16 
TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.13         0.07         0.10         0.10         0.20         1.18 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        5.16         3.78         9.30         4.80         8.48         4.44 
TCGA-VR-A8Q7 
       36.72 

$`DEL PEAK 39(17Q25.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
       13.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03         0.36         0.13        14.86         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        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        15.48        23.18        25.28        18.08        17.59 
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-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.52         3.68         8.78         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        30.74         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NF 
        6.94         8.71         2.60        25.12         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        5.42        21.37        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36         0.07        10.45         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 
        0.10         0.07         0.10         0.07         0.10         0.13 
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-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       17.62         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59         6.35        53.95         7.00         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G 
        5.29         3.42         8.15        18.31         8.12        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                          55.5                          122.1 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                          4.44                           8.12 
[1] "0.0 - 55.5 (4.4)"  "0.1 - 122.1 (8.1)"
[1] "hr=" "1.6"
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(17Q25.3) MUTATED         3        1        2        1        10
  DEL PEAK 39(17Q25.3) WILD-TYPE       5        3        4        0        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(17Q25.3) MUTATED           6         5          1          2
  DEL PEAK 39(17Q25.3) WILD-TYPE        20        18         10          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 39(17Q25.3) MUTATED            0        0         0
  DEL PEAK 39(17Q25.3) WILD-TYPE          6        3         2
D70V3, multiclass
            clus
vv           DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              1                              3
  STAGE IB                              2                              4
  STAGE II                              1                              0
  STAGE IIA                            10                             25
  STAGE IIB                             6                             20
  STAGE III                             5                             18
  STAGE IIIA                            1                             10
  STAGE IIIB                            2                              6
  STAGE IIIC                            0                              6
  STAGE IV                              0                              3
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 39(17Q25.3) MUTATED       7  9 17  0
  DEL PEAK 39(17Q25.3) WILD-TYPE    19 24 57  4
D70V4, multiclass
       clus
vv      DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  T0+T1                            7                             19
  T2                               9                             24
  T3                              17                             57
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 39(17Q25.3) MUTATED   19 11  2  0
  DEL PEAK 39(17Q25.3) WILD-TYPE 45 43  9  6
D70V5, multiclass
    clus
vv   DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  N0                           19                             45
  N1                           11                             43
  N2                            2                              9
  N3                            0                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 39(17Q25.3) MUTATED   30  0   0  3
  DEL PEAK 39(17Q25.3) WILD-TYPE 81  2   3 14
D70V6, multiclass
     clus
vv    DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  M0                            30                             81
  M1                             0                              2
  M1A                            0                              3
  MX                             3                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q25.3) MUTATED     6  29
  DEL PEAK 39(17Q25.3) WILD-TYPE  15 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q25.3) MUTATED      6   29
  DEL PEAK 39(17Q25.3) WILD-TYPE   15  100
        clus
vv       DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  FEMALE                            6                             15
  MALE                             29                            100
[1] 2 2
[1] FALSE
D70V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(17Q25.3) MUTATED      12                         1    20
  DEL PEAK 39(17Q25.3) WILD-TYPE    26                         1    73
D70V9, multiclass
                           clus
vv                          DEL PEAK 39(17Q25.3) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               20
                           clus
vv                          DEL PEAK 39(17Q25.3) WILD-TYPE
  ASIAN                                                 26
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = DEL PEAK 40(18P11.23) MUTATION ANALYSIS
D71V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 40(18P11.23) MUTATED   29 20
  DEL PEAK 40(18P11.23) WILD-TYPE 59 34
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             49                              93 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             20                              34 
$`DEL PEAK 40(18P11.23) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3I8 
       25.78        14.30         5.92         8.94        16.24        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
        0.85         2.63         0.79        23.41         0.43        44.75 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43E TCGA-L5-A43H 
       23.18        25.28        18.08        17.59         3.45         0.30 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A88S 
        3.52         3.68         3.35        19.50         7.17         6.94 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.95        55.50         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L 
       13.55        13.22         8.71        52.57         0.07        10.45 
TCGA-LN-A49N TCGA-LN-A49Y TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6XG 
        0.07         0.07         5.16         3.78         7.59        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-AASW TCGA-VR-A8EW 
        6.35         9.30         7.00         8.78         8.15         8.12 
TCGA-ZR-A9CJ 
       18.12 

$`DEL PEAK 40(18P11.23) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR 
       31.27        58.55         7.63        13.94         4.21        32.45 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09        20.78        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03         0.36         0.13        14.86         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M 
       25.41        15.48         6.21         3.16         4.31         8.94 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        8.78         6.41         4.08        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.74         4.90        29.00         7.13         7.43 
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-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
       13.48         7.76         5.42        21.37        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R 
       83.24        46.09        10.36         0.16         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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-R6-A6DN 
        0.10         0.07         0.20         1.18        17.62         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RB 
        5.06        14.70         7.04        53.95        14.01         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 
        3.42         4.80         8.48         4.44        18.31        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.03         9.17        15.91 

  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                           55.5                           122.1 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                           8.71                            7.04 
[1] "0.1 - 55.5 (8.7)"  "0.0 - 122.1 (7.0)"
[1] "hr=" "1.1"
D71V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(18P11.23) MUTATED         3        1        3        0         8
  DEL PEAK 40(18P11.23) WILD-TYPE       5        3        3        1        27
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18P11.23) MUTATED           6        10          4          5
  DEL PEAK 40(18P11.23) WILD-TYPE        20        13          7          3
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 40(18P11.23) MUTATED            2        1         2
  DEL PEAK 40(18P11.23) WILD-TYPE          4        2         0
D71V3, multiclass
            clus
vv           DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  STAGE I                                3                               5
  STAGE IA                               1                               3
  STAGE IB                               3                               3
  STAGE II                               0                               1
  STAGE IIA                              8                              27
  STAGE IIB                              6                              20
  STAGE III                             10                              13
  STAGE IIIA                             4                               7
  STAGE IIIB                             5                               3
  STAGE IIIC                             2                               4
  STAGE IV                               1                               2
  STAGE IVA                              2                               0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 40(18P11.23) MUTATED       8  6 31  1
  DEL PEAK 40(18P11.23) WILD-TYPE    18 27 43  3
D71V4, multiclass
       clus
vv      DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  T0+T1                             8                              18
  T2                                6                              27
  T3                               31                              43
  T4                                1                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 40(18P11.23) MUTATED   18 20  5  2
  DEL PEAK 40(18P11.23) WILD-TYPE 46 34  6  4
D71V5, multiclass
    clus
vv   DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  N0                            18                              46
  N1                            20                              34
  N2                             5                               6
  N3                             2                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  DEL PEAK 40(18P11.23) MUTATED   37  1   2  4
  DEL PEAK 40(18P11.23) WILD-TYPE 74  1   1 13
D71V6, multiclass
     clus
vv    DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  M0                             37                              74
  M1                              1                               1
  M1A                             2                               1
  MX                              4                              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                                 cls
clus                               0  1
  DEL PEAK 40(18P11.23) MUTATED   10 41
  DEL PEAK 40(18P11.23) WILD-TYPE 11 88
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.23) MUTATED     10   41
  DEL PEAK 40(18P11.23) WILD-TYPE   11   88
        clus
vv       DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  FEMALE                            10                              11
  MALE                              41                              88
[1] 2 2
[1] FALSE
D71V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(18P11.23) MUTATED      10                         0    35
  DEL PEAK 40(18P11.23) WILD-TYPE    28                         2    58
D71V9, multiclass
                           clus
vv                          DEL PEAK 40(18P11.23) MUTATED
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                35
                           clus
vv                          DEL PEAK 40(18P11.23) WILD-TYPE
  ASIAN                                                  28
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = DEL PEAK 41(18Q12.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 41(18Q12.2) MUTATED   50 35
  DEL PEAK 41(18Q12.2) WILD-TYPE 38 19
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                            85                             57 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                            35                             19 
$`DEL PEAK 41(18Q12.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        58.55         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       32.45         0.85         2.63         0.26         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       23.41         0.13         0.43        68.02         3.68        42.77 
TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       25.41        23.18        25.28        18.08        17.59         3.16 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         8.94         3.52         3.68         3.35        19.50 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         7.17         3.16         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        7.43         6.94         2.60         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        10.36        10.45         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 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-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07        17.62         5.16         3.78         8.02         7.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        6.35        53.95         7.00         8.78         5.29         3.42 
TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.15        18.31         8.12        12.03         9.17        15.91 
TCGA-ZR-A9CJ 
       18.12 

$`DEL PEAK 41(18Q12.2) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3QL 
       14.30         7.63         5.92        13.94        33.27        20.09 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
       20.78        20.12         0.03         0.99        17.03         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG 
       14.86         0.46       122.10        44.75        60.39        41.52 
TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OJ 
       15.48         6.21         3.45         4.31         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A88T TCGA-L5-A88W 
        4.08        18.35         1.38        30.74         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW TCGA-LN-A49K 
        0.36         7.40         7.76         5.42        46.09         0.07 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.13         0.10         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6KZ 
        0.10         0.07         0.07         0.20         1.18         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-S8-A6BW TCGA-V5-A7RE 
       14.70         7.04        29.59         9.30        14.01         4.80 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8Q7 
        8.48         4.44        36.72 

  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                          8.02                           7.04 
[1] "0.1 - 83.2 (8.0)"  "0.0 - 122.1 (7.0)"
[1] "hr=" "1.2"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(18Q12.2) MUTATED         4        2        3        1        20
  DEL PEAK 41(18Q12.2) WILD-TYPE       4        2        3        0        15
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(18Q12.2) MUTATED          13        15          6          6
  DEL PEAK 41(18Q12.2) WILD-TYPE        13         8          5          2
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 41(18Q12.2) MUTATED            5        3         2
  DEL PEAK 41(18Q12.2) WILD-TYPE          1        0         0
D72V3, multiclass
            clus
vv           DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              2
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                            20                             15
  STAGE IIB                            13                             13
  STAGE III                            15                              8
  STAGE IIIA                            6                              5
  STAGE IIIB                            6                              2
  STAGE IIIC                            5                              1
  STAGE IV                              3                              0
  STAGE IVA                             2                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 41(18Q12.2) MUTATED      13 19 49  2
  DEL PEAK 41(18Q12.2) WILD-TYPE    13 14 25  2
D72V4, multiclass
       clus
vv      DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  T0+T1                           13                             13
  T2                              19                             14
  T3                              49                             25
  T4                               2                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 41(18Q12.2) MUTATED   37 32  8  5
  DEL PEAK 41(18Q12.2) WILD-TYPE 27 22  3  1
D72V5, multiclass
    clus
vv   DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  N0                           37                             27
  N1                           32                             22
  N2                            8                              3
  N3                            5                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 41(18Q12.2) MUTATED   67  2   3  9
  DEL PEAK 41(18Q12.2) WILD-TYPE 44  0   0  8
D72V6, multiclass
     clus
vv    DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  M0                            67                             44
  M1                             2                              0
  M1A                            3                              0
  MX                             9                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q12.2) MUTATED   14 76
  DEL PEAK 41(18Q12.2) WILD-TYPE  7 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED     14   76
  DEL PEAK 41(18Q12.2) WILD-TYPE    7   53
        clus
vv       DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  FEMALE                           14                              7
  MALE                             76                             53
[1] 2 2
[1] FALSE
D72V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q12.2) MUTATED      20                         1    56
  DEL PEAK 41(18Q12.2) WILD-TYPE    18                         1    37
D72V9, multiclass
                           clus
vv                          DEL PEAK 41(18Q12.2) MUTATED
  ASIAN                                               20
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               56
                           clus
vv                          DEL PEAK 41(18Q12.2) WILD-TYPE
  ASIAN                                                 18
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = DEL PEAK 42(18Q21.2) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 42(18Q21.2) MUTATED   55 37
  DEL PEAK 42(18Q21.2) WILD-TYPE 33 17
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            92                             50 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            37                             17 
$`DEL PEAK 42(18Q21.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 
        8.94        16.24        32.45         0.85         2.63         0.03 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
        0.26         0.53         0.79        23.41         0.13         0.43 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        42.77        25.41        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
       18.08        17.59         3.16         0.30         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
        3.68         3.35        19.50         6.41         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16         4.90        29.00         7.43         6.94         2.60 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.55        13.22        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        27.12        83.24        52.57        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y 
        0.16         0.07         0.33         0.10         0.07         0.07 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.10         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-A6XG 
       17.62         5.16         3.78         8.02         7.59        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 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D 
        4.80         8.15        18.31         8.12        12.03         9.17 
TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.91        18.12 

$`DEL PEAK 42(18Q21.2) WILD-TYPE`
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
        5.92         4.21        33.27        20.09        20.78        20.12 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.99        17.03         0.36        14.86         0.46       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E 
       44.75        60.39        41.52        15.48         6.21         3.45 
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
        4.31         8.78         4.08        18.35         1.38        30.74 
TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NM 
        7.13         8.71        25.12         0.36         7.40         7.76 
TCGA-L5-A8NN TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        5.42        46.09         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 TCGA-V5-A7RC TCGA-V5-AASV 
        5.06        14.70         7.04        14.01         3.42         8.48 
TCGA-V5-AASX TCGA-VR-A8Q7 
        4.44        36.72 

  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                         8.070                          6.625 
[1] "0.0 - 83.2 (8.1)"  "0.1 - 122.1 (6.6)"
[1] "hr=" "1.1"
D73V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(18Q21.2) MUTATED         5        2        4        1        20
  DEL PEAK 42(18Q21.2) WILD-TYPE       3        2        2        0        15
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(18Q21.2) MUTATED          15        16          6          6
  DEL PEAK 42(18Q21.2) WILD-TYPE        11         7          5          2
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 42(18Q21.2) MUTATED            5        3         2
  DEL PEAK 42(18Q21.2) WILD-TYPE          1        0         0
D73V3, multiclass
            clus
vv           DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              2                              2
  STAGE IB                              4                              2
  STAGE II                              1                              0
  STAGE IIA                            20                             15
  STAGE IIB                            15                             11
  STAGE III                            16                              7
  STAGE IIIA                            6                              5
  STAGE IIIB                            6                              2
  STAGE IIIC                            5                              1
  STAGE IV                              3                              0
  STAGE IVA                             2                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 42(18Q21.2) MUTATED      16 20 50  2
  DEL PEAK 42(18Q21.2) WILD-TYPE    10 13 24  2
D73V4, multiclass
       clus
vv      DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  T0+T1                           16                             10
  T2                              20                             13
  T3                              50                             24
  T4                               2                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 42(18Q21.2) MUTATED   39 35  8  5
  DEL PEAK 42(18Q21.2) WILD-TYPE 25 19  3  1
D73V5, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  N0                           39                             25
  N1                           35                             19
  N2                            8                              3
  N3                            5                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 42(18Q21.2) MUTATED   72  2   3  9
  DEL PEAK 42(18Q21.2) WILD-TYPE 39  0   0  8
D73V6, multiclass
     clus
vv    DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  M0                            72                             39
  M1                             2                              0
  M1A                            3                              0
  MX                             9                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                                cls
clus                              0  1
  DEL PEAK 42(18Q21.2) MUTATED   14 82
  DEL PEAK 42(18Q21.2) WILD-TYPE  7 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED     14   82
  DEL PEAK 42(18Q21.2) WILD-TYPE    7   47
        clus
vv       DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  FEMALE                           14                              7
  MALE                             82                             47
[1] 2 2
[1] FALSE
D73V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(18Q21.2) MUTATED      21                         0    61
  DEL PEAK 42(18Q21.2) WILD-TYPE    17                         2    32
D73V9, multiclass
                           clus
vv                          DEL PEAK 42(18Q21.2) MUTATED
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               61
                           clus
vv                          DEL PEAK 42(18Q21.2) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = DEL PEAK 43(18Q22.3) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 43(18Q22.3) MUTATED   52 33
  DEL PEAK 43(18Q22.3) WILD-TYPE 36 21
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                            85                             57 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                            33                             21 
$`DEL PEAK 43(18Q22.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L 
       32.45        33.27         0.85         2.63         0.03         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD 
        0.79        23.41         0.13         0.43        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        42.77        25.41        23.18        25.28        18.08 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       17.59         3.16         0.30         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT 
        3.35        19.50         6.41         3.32         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
       29.00         7.43         6.94         2.60         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        35.97        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       52.57        10.36         0.16         0.07         0.33         0.10 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.07         0.07         0.10         0.10         0.07         0.20 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG 
       17.62         5.16         3.78         8.02         7.59        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW 
        6.35         9.30         7.00         8.78         5.29         8.15 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.31         8.12        36.72        12.03         9.17        15.91 
TCGA-ZR-A9CJ 
       18.12 

$`DEL PEAK 43(18Q22.3) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3YA 
       58.55         5.92        13.94         4.21        20.09        20.78 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP 
       20.12         0.26         0.99        17.03         0.36        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC 
        0.46       122.10        60.39        41.52        15.48         6.21 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        3.45         4.31         8.78         4.08        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        1.38        30.74         7.13         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW TCGA-LN-A49K 
        7.40        13.48         7.76         5.42        46.09         0.07 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 
       10.45         0.13         0.07         0.10         0.10         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 
        0.07         0.10         0.10         0.07         0.07         1.18 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RC 
        5.06        14.70         7.04        53.95        14.01         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        4.80         8.48         4.44 

  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                          8.15                           6.21 
[1] "0.0 - 83.2 (8.2)"  "0.1 - 122.1 (6.2)"
[1] "hr=" "1"  
D74V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(18Q22.3) MUTATED         4        1        3        1        18
  DEL PEAK 43(18Q22.3) WILD-TYPE       4        3        3        0        17
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q22.3) MUTATED          15        15          7          5
  DEL PEAK 43(18Q22.3) WILD-TYPE        11         8          4          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 43(18Q22.3) MUTATED            5        3         2
  DEL PEAK 43(18Q22.3) WILD-TYPE          1        0         0
D74V3, multiclass
            clus
vv           DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              3
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                            18                             17
  STAGE IIB                            15                             11
  STAGE III                            15                              8
  STAGE IIIA                            7                              4
  STAGE IIIB                            5                              3
  STAGE IIIC                            5                              1
  STAGE IV                              3                              0
  STAGE IVA                             2                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 43(18Q22.3) MUTATED      12 18 50  2
  DEL PEAK 43(18Q22.3) WILD-TYPE    14 15 24  2
D74V4, multiclass
       clus
vv      DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  T0+T1                           12                             14
  T2                              18                             15
  T3                              50                             24
  T4                               2                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 43(18Q22.3) MUTATED   34 35  7  5
  DEL PEAK 43(18Q22.3) WILD-TYPE 30 19  4  1
D74V5, multiclass
    clus
vv   DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  N0                           34                             30
  N1                           35                             19
  N2                            7                              4
  N3                            5                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 43(18Q22.3) MUTATED   67  2   3  8
  DEL PEAK 43(18Q22.3) WILD-TYPE 44  0   0  9
D74V6, multiclass
     clus
vv    DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  M0                            67                             44
  M1                             2                              0
  M1A                            3                              0
  MX                             8                              9
[1] 4 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 43(18Q22.3) MUTATED   14 75
  DEL PEAK 43(18Q22.3) WILD-TYPE  7 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.3) MUTATED     14   75
  DEL PEAK 43(18Q22.3) WILD-TYPE    7   54
        clus
vv       DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  FEMALE                           14                              7
  MALE                             75                             54
[1] 2 2
[1] FALSE
D74V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(18Q22.3) MUTATED      19                         0    58
  DEL PEAK 43(18Q22.3) WILD-TYPE    19                         2    35
D74V9, multiclass
                           clus
vv                          DEL PEAK 43(18Q22.3) MUTATED
  ASIAN                                               19
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               58
                           clus
vv                          DEL PEAK 43(18Q22.3) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = DEL PEAK 44(19P13.3) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 44(19P13.3) MUTATED   47 25
  DEL PEAK 44(19P13.3) WILD-TYPE 41 29
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            72                             70 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            25                             29 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
        8.94        16.24         4.21         2.63         0.03         0.26 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H 
        0.53        17.03         0.79        23.41         0.46         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E 
      122.10        68.02        42.77        25.41        23.18        18.08 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.45         8.94         3.52         3.68        19.50         4.08 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y 
        3.32         7.17        30.74         7.43         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.95         2.66        35.97        12.92        16.47        13.55 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        5.42         8.71        13.41        52.57        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       10.45         0.16         0.10         0.13         0.07         0.07 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 
        0.07         0.13         0.07         0.10         0.10         0.20 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-V5-A7RC TCGA-V5-A7RE 
        8.02         5.06         7.04        29.59         3.42         4.80 
TCGA-V5-AASW TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.15         8.12        36.72         9.17        15.91        18.12 

$`DEL PEAK 44(19P13.3) WILD-TYPE`
TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        5.92        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA 
       20.12         0.99         0.36         0.13        14.86        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
       60.39         3.68        41.52        15.48        25.28        17.59 
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-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NT 
       55.50        13.48        13.22         7.76        21.37        27.12 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49X 
       83.24         0.07         0.07         0.33         0.10         0.10 
TCGA-LN-A4A4 TCGA-LN-A4A5 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-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6XQ 
       17.62         5.16         3.78         7.59        14.70         6.35 
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 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-AA4G 
        8.48         4.44        18.31        12.03 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                         7.825                          7.265 
[1] "0.0 - 122.1 (7.8)" "0.1 - 83.2 (7.3)" 
[1] "hr=" "1.2"
D75V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(19P13.3) MUTATED         4        2        3        1        13
  DEL PEAK 44(19P13.3) WILD-TYPE       4        2        3        0        22
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(19P13.3) MUTATED          12        15          4          5
  DEL PEAK 44(19P13.3) WILD-TYPE        14         8          7          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 44(19P13.3) MUTATED            4        1         2
  DEL PEAK 44(19P13.3) WILD-TYPE          2        2         0
D75V3, multiclass
            clus
vv           DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              2
  STAGE IB                              3                              3
  STAGE II                              1                              0
  STAGE IIA                            13                             22
  STAGE IIB                            12                             14
  STAGE III                            15                              8
  STAGE IIIA                            4                              7
  STAGE IIIB                            5                              3
  STAGE IIIC                            4                              2
  STAGE IV                              1                              2
  STAGE IVA                             2                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 44(19P13.3) MUTATED      14 12 42  1
  DEL PEAK 44(19P13.3) WILD-TYPE    12 21 32  3
D75V4, multiclass
       clus
vv      DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  T0+T1                           14                             12
  T2                              12                             21
  T3                              42                             32
  T4                               1                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 44(19P13.3) MUTATED   28 30  6  4
  DEL PEAK 44(19P13.3) WILD-TYPE 36 24  5  2
D75V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  N0                           28                             36
  N1                           30                             24
  N2                            6                              5
  N3                            4                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 44(19P13.3) MUTATED   57  1   2  6
  DEL PEAK 44(19P13.3) WILD-TYPE 54  1   1 11
D75V6, multiclass
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  M0                            57                             54
  M1                             1                              1
  M1A                            2                              1
  MX                             6                             11
[1] 4 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 44(19P13.3) MUTATED    8 67
  DEL PEAK 44(19P13.3) WILD-TYPE 13 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      8   67
  DEL PEAK 44(19P13.3) WILD-TYPE   13   62
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  FEMALE                            8                             13
  MALE                             67                             62
[1] 2 2
[1] FALSE
D75V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(19P13.3) MUTATED      21                         1    41
  DEL PEAK 44(19P13.3) WILD-TYPE    17                         1    52
D75V9, multiclass
                           clus
vv                          DEL PEAK 44(19P13.3) MUTATED
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               41
                           clus
vv                          DEL PEAK 44(19P13.3) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = DEL PEAK 45(19Q11) MUTATION ANALYSIS
D76V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 45(19Q11) MUTATED   22 15
  DEL PEAK 45(19Q11) WILD-TYPE 66 39
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                          37                          105 
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                          15                           39 
$`DEL PEAK 45(19Q11) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A6QS 
       25.78        14.30        16.24         4.21         2.63         0.13 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OM 
       68.02         3.68        42.77         3.45         4.31         4.08 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL 
        7.17        30.74         7.43         2.66        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
        5.42        46.09         0.16         0.10         0.13         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6L6 
        0.07         0.13         0.07         0.20         8.02         7.04 
TCGA-R6-A6Y0 TCGA-V5-A7RB TCGA-V5-AASW TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7D 
       53.95         5.29         8.15         8.12        36.72         9.17 
TCGA-ZR-A9CJ 
       18.12 

$`DEL PEAK 45(19Q11) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
       32.45        33.27        20.09         0.85        20.78        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-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       23.41         0.36        14.86         0.46         0.43       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       44.75        60.39        41.52        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       25.28        18.08        17.59         6.21         3.16         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94         3.52         3.68         3.35        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
        6.41        18.35         3.32         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG 
        0.36         7.40         3.95         3.02        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       12.92        13.48        13.55         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       10.45         0.07         0.33         0.07         0.07         0.10 
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-Q9-A6FW TCGA-R6-A6DQ 
        0.07         1.18        17.62         5.16         3.78         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        5.06        14.70        29.59         6.35         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        8.78        14.01         3.42         4.80         8.48         4.44 
TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7I 
       18.31        12.03        15.91 

  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                        0.07                         0.03 
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                       68.02                       122.10 
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                        7.04                         7.76 
[1] "0.1 - 68.0 (7.0)"  "0.0 - 122.1 (7.8)"
[1] "hr=" "1.2"
D76V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(19Q11) MUTATED         1        2        1        0         9
  DEL PEAK 45(19Q11) WILD-TYPE       7        2        5        1        26
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(19Q11) MUTATED           6         9          2          1
  DEL PEAK 45(19Q11) WILD-TYPE        20        14          9          7
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 45(19Q11) MUTATED            2        0         2
  DEL PEAK 45(19Q11) WILD-TYPE          4        3         0
D76V3, multiclass
            clus
vv           DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  STAGE I                             1                            7
  STAGE IA                            2                            2
  STAGE IB                            1                            5
  STAGE II                            0                            1
  STAGE IIA                           9                           26
  STAGE IIB                           6                           20
  STAGE III                           9                           14
  STAGE IIIA                          2                            9
  STAGE IIIB                          1                            7
  STAGE IIIC                          2                            4
  STAGE IV                            0                            3
  STAGE IVA                           2                            0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 45(19Q11) MUTATED       5  9 22  0
  DEL PEAK 45(19Q11) WILD-TYPE    21 24 52  4
D76V4, multiclass
       clus
vv      DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  T0+T1                          5                           21
  T2                             9                           24
  T3                            22                           52
  T4                             0                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 45(19Q11) MUTATED   14 19  1  2
  DEL PEAK 45(19Q11) WILD-TYPE 50 35 10  4
D76V5, multiclass
    clus
vv   DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  N0                         14                           50
  N1                         19                           35
  N2                          1                           10
  N3                          2                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 M1A MX
  DEL PEAK 45(19Q11) MUTATED   29  0   2  4
  DEL PEAK 45(19Q11) WILD-TYPE 82  2   1 13
D76V6, multiclass
     clus
vv    DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  M0                          29                           82
  M1                           0                            2
  M1A                          2                            1
  MX                           4                           13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                              cls
clus                            0  1
  DEL PEAK 45(19Q11) MUTATED    4 36
  DEL PEAK 45(19Q11) WILD-TYPE 17 93
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(19Q11) MUTATED      4   36
  DEL PEAK 45(19Q11) WILD-TYPE   17   93
        clus
vv       DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  FEMALE                          4                           17
  MALE                           36                           93
[1] 2 2
[1] FALSE
D76V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(19Q11) MUTATED      13                         0    21
  DEL PEAK 45(19Q11) WILD-TYPE    25                         2    72
D76V9, multiclass
                           clus
vv                          DEL PEAK 45(19Q11) MUTATED
  ASIAN                                             13
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             21
                           clus
vv                          DEL PEAK 45(19Q11) WILD-TYPE
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = DEL PEAK 46(20P12.1) MUTATION ANALYSIS
D77V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 46(20P12.1) MUTATED   21  7
  DEL PEAK 46(20P12.1) WILD-TYPE 67 47
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            28                            114 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                             7                             47 
$`DEL PEAK 46(20P12.1) MUTATED`
TCGA-2H-A9GI TCGA-IG-A4QS TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A938 
       14.30         0.26        44.75        68.02        42.77        25.41 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NE TCGA-L5-A8NF 
        8.94         3.68        19.50         3.32        55.50         2.66 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
       16.47        13.22         8.71        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49Y TCGA-R6-A6KZ TCGA-R6-A6XG 
       10.45         0.16         0.33         0.07         5.06        29.59 
TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
       53.95        14.01        36.72        18.12 

$`DEL PEAK 46(20P12.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         0.03         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE 
       14.86         0.46         0.43       122.10        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        15.48        23.18        25.28        18.08        17.59 
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-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        3.35         8.78         6.41         4.08        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.95         3.02        35.97        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NV 
       13.55         7.76         5.42        21.37        27.12        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       46.09         0.07         0.07         0.10         0.13         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-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-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.20         1.18        17.62         5.16         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.59        14.70         7.04         6.35         9.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        8.78         5.29         3.42         4.80         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        4.44        18.31         8.12        12.03         9.17        15.91 

  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                         13.71                           6.97 
[1] "0.1 - 83.2 (13.7)" "0.0 - 122.1 (7.0)"
[1] "hr=" "2.9"
D77V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(20P12.1) MUTATED         1        0        1        0         7
  DEL PEAK 46(20P12.1) WILD-TYPE       7        4        5        1        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(20P12.1) MUTATED           6         5          1          1
  DEL PEAK 46(20P12.1) WILD-TYPE        20        18         10          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 46(20P12.1) MUTATED            3        0         1
  DEL PEAK 46(20P12.1) WILD-TYPE          3        3         1
D77V3, multiclass
            clus
vv           DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              0                              4
  STAGE IB                              1                              5
  STAGE II                              0                              1
  STAGE IIA                             7                             28
  STAGE IIB                             6                             20
  STAGE III                             5                             18
  STAGE IIIA                            1                             10
  STAGE IIIB                            1                              7
  STAGE IIIC                            3                              3
  STAGE IV                              0                              3
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 46(20P12.1) MUTATED       3  8 16  0
  DEL PEAK 46(20P12.1) WILD-TYPE    23 25 58  4
D77V4, multiclass
       clus
vv      DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  T0+T1                            3                             23
  T2                               8                             25
  T3                              16                             58
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 46(20P12.1) MUTATED   12 10  2  3
  DEL PEAK 46(20P12.1) WILD-TYPE 52 44  9  3
D77V5, multiclass
    clus
vv   DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  N0                           12                             52
  N1                           10                             44
  N2                            2                              9
  N3                            3                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 46(20P12.1) MUTATED   21  0   1  4
  DEL PEAK 46(20P12.1) WILD-TYPE 90  2   2 13
D77V6, multiclass
     clus
vv    DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  M0                            21                             90
  M1                             0                              2
  M1A                            1                              2
  MX                             4                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED     3  27
  DEL PEAK 46(20P12.1) WILD-TYPE  18 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED      3   27
  DEL PEAK 46(20P12.1) WILD-TYPE   18  102
        clus
vv       DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  FEMALE                            3                             18
  MALE                             27                            102
[1] 2 2
[1] FALSE
D77V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(20P12.1) MUTATED       8                         0    19
  DEL PEAK 46(20P12.1) WILD-TYPE    30                         2    74
D77V9, multiclass
                           clus
vv                          DEL PEAK 46(20P12.1) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               19
                           clus
vv                          DEL PEAK 46(20P12.1) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = DEL PEAK 47(21Q11.2) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 47(21Q11.2) MUTATED   55 27
  DEL PEAK 47(21Q11.2) WILD-TYPE 33 27
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            82                             60 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            27                             27 
$`DEL PEAK 47(21Q11.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78         7.63         5.92        13.94        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        0.85        20.78        20.12         0.03         0.26         0.53 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A93C TCGA-JY-A93D 
        0.79         0.13       122.10        68.02        23.18        25.28 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       17.59         3.16         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
        3.52         3.68         3.35        19.50         4.08        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-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        6.94         2.60         0.36         7.40         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
        2.66        12.92        16.47        13.55        13.22         5.42 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        52.57        46.09        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 TCGA-V5-AASW 
       29.59         6.35         9.30        14.01         4.80         8.15 
TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
        4.44         8.12        36.72        18.12 

$`DEL PEAK 47(21Q11.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30        58.55         8.94        16.24         4.21 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
       20.09         2.63         0.99        17.03        23.41         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
       14.86         0.46         0.43        44.75        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC 
       41.52        42.77        25.41        15.48        18.08         6.21 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A88T 
        8.78         6.41         3.32         1.38         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ 
       25.12        55.50        35.97        13.48         7.76        21.37 
TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
       83.24        10.45         0.16         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-Q9-A6FU 
        0.13         0.10         0.07         0.10         1.18         5.16 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        7.59        14.70        53.95         7.00         8.78         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        3.42         8.48        18.31        12.03         9.17        15.91 

  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                         6.645                          8.780 
[1] "0.0 - 122.1 (6.6)" "0.1 - 83.2 (8.8)" 
[1] "hr=" "1.1"
D78V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(21Q11.2) MUTATED         5        3        6        1        19
  DEL PEAK 47(21Q11.2) WILD-TYPE       3        1        0        0        16
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(21Q11.2) MUTATED          12        13          5          5
  DEL PEAK 47(21Q11.2) WILD-TYPE        14        10          6          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 47(21Q11.2) MUTATED            3        2         1
  DEL PEAK 47(21Q11.2) WILD-TYPE          3        1         1
D78V3, multiclass
            clus
vv           DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              3                              1
  STAGE IB                              6                              0
  STAGE II                              1                              0
  STAGE IIA                            19                             16
  STAGE IIB                            12                             14
  STAGE III                            13                             10
  STAGE IIIA                            5                              6
  STAGE IIIB                            5                              3
  STAGE IIIC                            3                              3
  STAGE IV                              2                              1
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 47(21Q11.2) MUTATED      16 18 42  2
  DEL PEAK 47(21Q11.2) WILD-TYPE    10 15 32  2
D78V4, multiclass
       clus
vv      DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  T0+T1                           16                             10
  T2                              18                             15
  T3                              42                             32
  T4                               2                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 47(21Q11.2) MUTATED   40 29  6  3
  DEL PEAK 47(21Q11.2) WILD-TYPE 24 25  5  3
D78V5, multiclass
    clus
vv   DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  N0                           40                             24
  N1                           29                             25
  N2                            6                              5
  N3                            3                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 47(21Q11.2) MUTATED   61  1   2 10
  DEL PEAK 47(21Q11.2) WILD-TYPE 50  1   1  7
D78V6, multiclass
     clus
vv    DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  M0                            61                             50
  M1                             1                              1
  M1A                            2                              1
  MX                            10                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                                cls
clus                              0  1
  DEL PEAK 47(21Q11.2) MUTATED   13 74
  DEL PEAK 47(21Q11.2) WILD-TYPE  8 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED     13   74
  DEL PEAK 47(21Q11.2) WILD-TYPE    8   55
        clus
vv       DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  FEMALE                           13                              8
  MALE                             74                             55
[1] 2 2
[1] FALSE
D78V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(21Q11.2) MUTATED      21                         0    57
  DEL PEAK 47(21Q11.2) WILD-TYPE    17                         2    36
D78V9, multiclass
                           clus
vv                          DEL PEAK 47(21Q11.2) MUTATED
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               57
                           clus
vv                          DEL PEAK 47(21Q11.2) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = DEL PEAK 48(21Q21.1) MUTATION ANALYSIS
D79V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 48(21Q21.1) MUTATED   53 29
  DEL PEAK 48(21Q21.1) WILD-TYPE 35 25
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                            82                             60 
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                            29                             25 
$`DEL PEAK 48(21Q21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78         7.63         5.92        13.94        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        0.85        20.78        20.12         0.03         0.26         0.53 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A93C TCGA-JY-A93D 
        0.79         0.13       122.10        68.02        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       18.08        17.59         3.16         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM 
        8.94         3.52         3.68         3.35        19.50         4.08 
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-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        7.43         6.94         2.60         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
        5.42         8.71        13.41        27.12        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.36         0.07         0.07         0.33         0.10         0.13 
TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.07         0.07         0.10         0.10         0.07         0.20 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
       17.62         3.78         8.02         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        6.35         9.30         3.42         4.80         8.15         4.44 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-ZR-A9CJ 
        8.12        36.72         9.17        18.12 

$`DEL PEAK 48(21Q21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30        58.55         8.94        16.24         4.21 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
       20.09         2.63         0.99        17.03        23.41         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
       14.86         0.46         0.43        44.75        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A4OI 
       41.52        42.77        25.41        15.48         6.21         8.78 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88T TCGA-L5-A88W 
        6.41        18.35         3.32         1.38         8.71        25.12 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU 
       55.50        35.97        13.48         7.76        21.37        83.24 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       10.45         0.16         0.07         0.10         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 
        0.13         0.10         0.10         0.07         0.07         1.18 
TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV 
        5.16         7.59        14.70        53.95         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7I 
       14.01         5.29         8.48        18.31        12.03        15.91 

  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                          6.99                           8.78 
[1] "0.0 - 122.1 (7.0)" "0.1 - 83.2 (8.8)" 
[1] "hr=" "1.1"
D79V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(21Q21.1) MUTATED         5        3        5        1        16
  DEL PEAK 48(21Q21.1) WILD-TYPE       3        1        1        0        19
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(21Q21.1) MUTATED          12        14          6          5
  DEL PEAK 48(21Q21.1) WILD-TYPE        14         9          5          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 48(21Q21.1) MUTATED            4        2         1
  DEL PEAK 48(21Q21.1) WILD-TYPE          2        1         1
D79V3, multiclass
            clus
vv           DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              3                              1
  STAGE IB                              5                              1
  STAGE II                              1                              0
  STAGE IIA                            16                             19
  STAGE IIB                            12                             14
  STAGE III                            14                              9
  STAGE IIIA                            6                              5
  STAGE IIIB                            5                              3
  STAGE IIIC                            4                              2
  STAGE IV                              2                              1
  STAGE IVA                             1                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 48(21Q21.1) MUTATED      15 16 44  2
  DEL PEAK 48(21Q21.1) WILD-TYPE    11 17 30  2
D79V4, multiclass
       clus
vv      DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  T0+T1                           15                             11
  T2                              16                             17
  T3                              44                             30
  T4                               2                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 48(21Q21.1) MUTATED   36 31  6  4
  DEL PEAK 48(21Q21.1) WILD-TYPE 28 23  5  2
D79V5, multiclass
    clus
vv   DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  N0                           36                             28
  N1                           31                             23
  N2                            6                              5
  N3                            4                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 48(21Q21.1) MUTATED   62  1   2  9
  DEL PEAK 48(21Q21.1) WILD-TYPE 49  1   1  8
D79V6, multiclass
     clus
vv    DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  M0                            62                             49
  M1                             1                              1
  M1A                            2                              1
  MX                             9                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                                cls
clus                              0  1
  DEL PEAK 48(21Q21.1) MUTATED   13 74
  DEL PEAK 48(21Q21.1) WILD-TYPE  8 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q21.1) MUTATED     13   74
  DEL PEAK 48(21Q21.1) WILD-TYPE    8   55
        clus
vv       DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  FEMALE                           13                              8
  MALE                             74                             55
[1] 2 2
[1] FALSE
D79V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 48(21Q21.1) MUTATED      19                         1    57
  DEL PEAK 48(21Q21.1) WILD-TYPE    19                         1    36
D79V9, multiclass
                           clus
vv                          DEL PEAK 48(21Q21.1) MUTATED
  ASIAN                                               19
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               57
                           clus
vv                          DEL PEAK 48(21Q21.1) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = DEL PEAK 49(21Q22.12) MUTATION ANALYSIS
D80V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 49(21Q22.12) MUTATED   51 32
  DEL PEAK 49(21Q22.12) WILD-TYPE 37 22
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                             83                              59 
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                             32                              22 
$`DEL PEAK 49(21Q22.12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR 
       25.78         7.63         5.92        13.94         8.94        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78        20.12         0.03         0.26 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        0.53         0.79         0.13       122.10        44.75        68.02 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        25.28        17.59         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        4.31         8.94         3.52         3.35        19.50         6.41 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        4.08         7.17         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         7.43         6.94         2.60         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.95         3.02         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       13.55        13.22         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       46.09        10.36         0.07         0.07         0.33         0.13 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.07         0.10         0.10         0.07         0.20 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
       17.62         3.78         8.02         7.59         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
       29.59         6.35         9.30         3.42         4.80         8.15 
TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-ZR-A9CJ 
        4.44         8.12        36.72         9.17        18.12 

$`DEL PEAK 49(21Q22.12) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL 
       31.27        14.30        58.55        16.24         4.21        20.09 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
        2.63         0.99        17.03        23.41         0.36        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        0.46         0.43        60.39         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OI 
       25.41        15.48        18.08         6.21         3.68         8.78 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NE 
       18.35         3.32         1.38         8.71        25.12        55.50 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L 
       13.48         7.76         5.42        21.37        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
        0.16         0.10         0.07         0.10         0.07         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 
        0.13         0.10         0.10         0.07         0.07         1.18 
TCGA-Q9-A6FU TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        5.16        14.70        53.95         7.00         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7I 
        5.29         8.48        18.31        12.03        15.91 

  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                           0.03                            0.07 
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                         122.10                           83.24 
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                           7.17                            8.71 
[1] "0.0 - 122.1 (7.2)" "0.1 - 83.2 (8.7)" 
[1] "hr=" "1.2"
D80V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(21Q22.12) MUTATED         6        3        5        1        16
  DEL PEAK 49(21Q22.12) WILD-TYPE       2        1        1        0        19
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(21Q22.12) MUTATED          12        13          5          5
  DEL PEAK 49(21Q22.12) WILD-TYPE        14        10          6          3
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 49(21Q22.12) MUTATED            4        2         1
  DEL PEAK 49(21Q22.12) WILD-TYPE          2        1         1
D80V3, multiclass
            clus
vv           DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  STAGE I                                6                               2
  STAGE IA                               3                               1
  STAGE IB                               5                               1
  STAGE II                               1                               0
  STAGE IIA                             16                              19
  STAGE IIB                             12                              14
  STAGE III                             13                              10
  STAGE IIIA                             5                               6
  STAGE IIIB                             5                               3
  STAGE IIIC                             4                               2
  STAGE IV                               2                               1
  STAGE IVA                              1                               1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 49(21Q22.12) MUTATED      15 16 43  2
  DEL PEAK 49(21Q22.12) WILD-TYPE    11 17 31  2
D80V4, multiclass
       clus
vv      DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  T0+T1                            15                              11
  T2                               16                              17
  T3                               43                              31
  T4                                2                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 49(21Q22.12) MUTATED   37 29  6  4
  DEL PEAK 49(21Q22.12) WILD-TYPE 27 25  5  2
D80V5, multiclass
    clus
vv   DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  N0                            37                              27
  N1                            29                              25
  N2                             6                               5
  N3                             4                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  DEL PEAK 49(21Q22.12) MUTATED   62  1   2  9
  DEL PEAK 49(21Q22.12) WILD-TYPE 49  1   1  8
D80V6, multiclass
     clus
vv    DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  M0                             62                              49
  M1                              1                               1
  M1A                             2                               1
  MX                              9                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                                 cls
clus                               0  1
  DEL PEAK 49(21Q22.12) MUTATED   15 72
  DEL PEAK 49(21Q22.12) WILD-TYPE  6 57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(21Q22.12) MUTATED     15   72
  DEL PEAK 49(21Q22.12) WILD-TYPE    6   57
        clus
vv       DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  FEMALE                            15                               6
  MALE                              72                              57
[1] 2 2
[1] FALSE
D80V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 49(21Q22.12) MUTATED      19                         1    56
  DEL PEAK 49(21Q22.12) WILD-TYPE    19                         1    37
D80V9, multiclass
                           clus
vv                          DEL PEAK 49(21Q22.12) MUTATED
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                56
                           clus
vv                          DEL PEAK 49(21Q22.12) WILD-TYPE
  ASIAN                                                  19
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = DEL PEAK 50(22Q11.1) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 50(22Q11.1) MUTATED   35 30
  DEL PEAK 50(22Q11.1) WILD-TYPE 53 24
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                            65                             77 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                            30                             24 
$`DEL PEAK 50(22Q11.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YB 
       13.94         8.94        16.24         4.21        32.45         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-JY-A6F8 
        0.03         0.26         0.53         0.79        23.41       122.10 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OG 
       42.77        25.41        25.28         3.16         3.52         3.35 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       19.50        18.35         7.17         3.16        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
       29.00         7.13         2.60         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.55        13.22         5.42         8.71        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
        0.07        10.45         0.33         0.10         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-RE-A7BO 
        0.10         0.07         8.02         7.59         5.06         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EU TCGA-ZR-A9CJ 
        5.29         4.80         8.15        18.31        18.12 

$`DEL PEAK 50(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-IG-A97H 
       17.03         0.36         0.13        14.86         0.46         0.43 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        15.48 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       23.18        18.08        17.59         6.21         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31         8.94         3.68         8.78         6.41         4.08 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        3.32         1.38         7.43         6.94         8.71        25.12 
TCGA-L5-A8NG TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       35.97         7.76        21.37        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y 
       52.57         0.16         0.07         0.13         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.13         0.10         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-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        3.78        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX 
        9.30         8.78        14.01         3.42         8.48         4.44 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.12        36.72        12.03         9.17        15.91 

  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                          7.59                           7.43 
[1] "0.0 - 122.1 (7.6)" "0.1 - 83.2 (7.4)" 
[1] "hr=" "1.5"
D81V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(22Q11.1) MUTATED         5        2        3        0        11
  DEL PEAK 50(22Q11.1) WILD-TYPE       3        2        3        1        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(22Q11.1) MUTATED          11        16          2          2
  DEL PEAK 50(22Q11.1) WILD-TYPE        15         7          9          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 50(22Q11.1) MUTATED            3        3         2
  DEL PEAK 50(22Q11.1) WILD-TYPE          3        0         0
D81V3, multiclass
            clus
vv           DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              2                              2
  STAGE IB                              3                              3
  STAGE II                              0                              1
  STAGE IIA                            11                             24
  STAGE IIB                            11                             15
  STAGE III                            16                              7
  STAGE IIIA                            2                              9
  STAGE IIIB                            2                              6
  STAGE IIIC                            3                              3
  STAGE IV                              3                              0
  STAGE IVA                             2                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 50(22Q11.1) MUTATED      18 10 35  0
  DEL PEAK 50(22Q11.1) WILD-TYPE     8 23 39  4
D81V4, multiclass
       clus
vv      DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  T0+T1                           18                              8
  T2                              10                             23
  T3                              35                             39
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 50(22Q11.1) MUTATED   24 34  2  3
  DEL PEAK 50(22Q11.1) WILD-TYPE 40 20  9  3
D81V5, multiclass
    clus
vv   DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  N0                           24                             40
  N1                           34                             20
  N2                            2                              9
  N3                            3                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 50(22Q11.1) MUTATED   49  2   3  7
  DEL PEAK 50(22Q11.1) WILD-TYPE 62  0   0 10
D81V6, multiclass
     clus
vv    DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  M0                            49                             62
  M1                             2                              0
  M1A                            3                              0
  MX                             7                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                                cls
clus                              0  1
  DEL PEAK 50(22Q11.1) MUTATED   11 57
  DEL PEAK 50(22Q11.1) WILD-TYPE 10 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 50(22Q11.1) MUTATED     11   57
  DEL PEAK 50(22Q11.1) WILD-TYPE   10   72
        clus
vv       DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  FEMALE                           11                             10
  MALE                             57                             72
[1] 2 2
[1] FALSE
D81V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 50(22Q11.1) MUTATED      12                         0    42
  DEL PEAK 50(22Q11.1) WILD-TYPE    26                         2    51
D81V9, multiclass
                           clus
vv                          DEL PEAK 50(22Q11.1) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               42
                           clus
vv                          DEL PEAK 50(22Q11.1) WILD-TYPE
  ASIAN                                                 26
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(82) Variable = DEL PEAK 51(XP21.1) MUTATION ANALYSIS
D82V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 51(XP21.1) MUTATED   31 19
  DEL PEAK 51(XP21.1) WILD-TYPE 57 35
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           50                            92 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           19                            35 
$`DEL PEAK 51(XP21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
       25.78        14.30         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        0.85        20.78         0.26         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A938 
        0.36         0.13         0.46        44.75        42.77        25.41 
TCGA-JY-A93C TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
       23.18         4.31         3.52         3.68         6.41         4.08 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NS 
       18.35         7.17         1.38         3.95        16.47        13.41 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 
        0.07         0.16         0.10         0.07         0.13         0.10 
TCGA-LN-A4MR 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-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        8.78         5.29         8.15         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA7I 
       36.72        15.91 

$`DEL PEAK 51(XP21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
       16.24         2.63        20.12         0.03         0.99         0.79 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         0.43       122.10        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        15.48        25.28        18.08        17.59         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-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        13.55        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.36        10.45         0.07         0.33         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.10         0.07         0.10         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.07         0.10         3.78         7.59         5.06 
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-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-AA4G 
        7.00        14.01         3.42         4.80         8.48        12.03 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                        44.75                        122.10 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                        5.850                         7.695 
[1] "0.1 - 44.8 (5.8)"  "0.0 - 122.1 (7.7)"
[1] "hr=" "1.3"
D82V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(XP21.1) MUTATED         1        2        0        0        15
  DEL PEAK 51(XP21.1) WILD-TYPE       7        2        6        1        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(XP21.1) MUTATED          12         6          6          7
  DEL PEAK 51(XP21.1) WILD-TYPE        14        17          5          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 51(XP21.1) MUTATED            0        1         0
  DEL PEAK 51(XP21.1) WILD-TYPE          6        2         2
D82V3, multiclass
            clus
vv           DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             2                             2
  STAGE IB                             0                             6
  STAGE II                             0                             1
  STAGE IIA                           15                            20
  STAGE IIB                           12                            14
  STAGE III                            6                            17
  STAGE IIIA                           6                             5
  STAGE IIIB                           7                             1
  STAGE IIIC                           0                             6
  STAGE IV                             1                             2
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 51(XP21.1) MUTATED       8 12 29  3
  DEL PEAK 51(XP21.1) WILD-TYPE    18 21 45  1
D82V4, multiclass
       clus
vv      DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  T0+T1                           8                            18
  T2                             12                            21
  T3                             29                            45
  T4                              3                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 51(XP21.1) MUTATED   26 18  8  0
  DEL PEAK 51(XP21.1) WILD-TYPE 38 36  3  6
D82V5, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  N0                          26                            38
  N1                          18                            36
  N2                           8                             3
  N3                           0                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 51(XP21.1) MUTATED   42  1   0  5
  DEL PEAK 51(XP21.1) WILD-TYPE 69  1   3 12
D82V6, multiclass
     clus
vv    DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  M0                           42                            69
  M1                            1                             1
  M1A                           0                             3
  MX                            5                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                               cls
clus                             0  1
  DEL PEAK 51(XP21.1) MUTATED    6 49
  DEL PEAK 51(XP21.1) WILD-TYPE 15 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED      6   49
  DEL PEAK 51(XP21.1) WILD-TYPE   15   80
        clus
vv       DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  FEMALE                           6                            15
  MALE                            49                            80
[1] 2 2
[1] FALSE
D82V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 51(XP21.1) MUTATED      20                         0    29
  DEL PEAK 51(XP21.1) WILD-TYPE    18                         2    64
D82V9, multiclass
                           clus
vv                          DEL PEAK 51(XP21.1) MUTATED
  ASIAN                                              20
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              29
                           clus
vv                          DEL PEAK 51(XP21.1) WILD-TYPE
  ASIAN                                                18
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(83) Variable = DEL PEAK 52(XP11.3) MUTATION ANALYSIS
D83V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 52(XP11.3) MUTATED   34 18
  DEL PEAK 52(XP11.3) WILD-TYPE 54 36
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           52                            90 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           18                            36 
$`DEL PEAK 52(XP11.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
       25.78        14.30         8.94         4.21        32.45        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.78        20.12         0.26         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA 
        0.79        23.41         0.36         0.13         0.46        44.75 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.41        23.18         4.31         3.52         3.68 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NJ 
        6.41         4.08        18.35         7.17         3.95        16.47 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49W 
        8.71        13.41         0.07         0.16         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.10         0.07         0.13         0.10         0.07         0.07 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-V5-AASW TCGA-V5-AASX 
        1.18        17.62         5.16         8.78         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I 
       18.31         8.12        36.72        15.91 

$`DEL PEAK 52(XP11.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       31.27        58.55         7.63         5.92        13.94        16.24 
TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A7DP TCGA-IG-A97H 
       33.27         2.63         0.03         0.99        14.86         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        60.39        68.02         3.68        41.52        15.48 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       25.28        18.08        17.59         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO 
        0.30         8.94         3.35        19.50         8.78         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.42        21.37 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       27.12        83.24        52.57        46.09        10.36        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A3 
        0.07         0.33         0.13         0.07         0.10         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-Q9-A6FW 
        0.10         0.10         0.07         0.10         0.20         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-A6BW TCGA-V5-A7RB 
        6.35        53.95         9.30         7.00        14.01         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
        3.42         4.80         8.48        12.03         9.17        18.12 

  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                        44.75                        122.10 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                        5.785                         7.695 
[1] "0.1 - 44.8 (5.8)"  "0.0 - 122.1 (7.7)"
[1] "hr=" "1.2"
D83V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XP11.3) MUTATED         1        2        1        0        17
  DEL PEAK 52(XP11.3) WILD-TYPE       7        2        5        1        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(XP11.3) MUTATED          11        10          6          7
  DEL PEAK 52(XP11.3) WILD-TYPE        15        13          5          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 52(XP11.3) MUTATED            0        1         0
  DEL PEAK 52(XP11.3) WILD-TYPE          6        2         2
D83V3, multiclass
            clus
vv           DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             2                             2
  STAGE IB                             1                             5
  STAGE II                             0                             1
  STAGE IIA                           17                            18
  STAGE IIB                           11                            15
  STAGE III                           10                            13
  STAGE IIIA                           6                             5
  STAGE IIIB                           7                             1
  STAGE IIIC                           0                             6
  STAGE IV                             1                             2
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 52(XP11.3) MUTATED       7 12 35  3
  DEL PEAK 52(XP11.3) WILD-TYPE    19 21 39  1
D83V4, multiclass
       clus
vv      DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  T0+T1                           7                            19
  T2                             12                            21
  T3                             35                            39
  T4                              3                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 52(XP11.3) MUTATED   29 21  7  0
  DEL PEAK 52(XP11.3) WILD-TYPE 35 33  4  6
D83V5, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  N0                          29                            35
  N1                          21                            33
  N2                           7                             4
  N3                           0                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 52(XP11.3) MUTATED   49  1   0  3
  DEL PEAK 52(XP11.3) WILD-TYPE 62  1   3 14
D83V6, multiclass
     clus
vv    DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  M0                           49                            62
  M1                            1                             1
  M1A                           0                             3
  MX                            3                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
                               cls
clus                             0  1
  DEL PEAK 52(XP11.3) MUTATED    6 53
  DEL PEAK 52(XP11.3) WILD-TYPE 15 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED      6   53
  DEL PEAK 52(XP11.3) WILD-TYPE   15   76
        clus
vv       DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  FEMALE                           6                            15
  MALE                            53                            76
[1] 2 2
[1] FALSE
D83V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 52(XP11.3) MUTATED      24                         0    28
  DEL PEAK 52(XP11.3) WILD-TYPE    14                         2    65
D83V9, multiclass
                           clus
vv                          DEL PEAK 52(XP11.3) MUTATED
  ASIAN                                              24
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              28
                           clus
vv                          DEL PEAK 52(XP11.3) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(84) Variable = DEL PEAK 53(XQ11.2) MUTATION ANALYSIS
D84V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 53(XQ11.2) MUTATED   24 10
  DEL PEAK 53(XQ11.2) WILD-TYPE 64 44
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                           34                           108 
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                           10                            44 
$`DEL PEAK 53(XQ11.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-IG-A3YC TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FH 
       25.78         4.21        20.12         0.13        44.75        42.77 
TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ 
       25.41        23.18         8.94         3.52         3.68         6.41 
TCGA-L5-A4OP TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.17         0.36         3.95        13.48        16.47        13.55 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49Y 
        8.71        13.41         0.07        10.45         0.16         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.13         0.10         1.18        17.62         5.16         3.78 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         8.15         4.44 

$`DEL PEAK 53(XQ11.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         0.36        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.43       122.10        60.39        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        3.45         0.30         4.31         3.35        19.50         8.78 
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-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-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       35.97        12.92        13.22         7.76         5.42        21.37 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49N 
       27.12        83.24        52.57        46.09        10.36         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-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.10         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.10         0.07         0.20         8.02         7.59         5.06 
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-A6BV TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EU 
        7.00         8.78        14.01         4.80         8.48        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.12        36.72        12.03         9.17        15.91        18.12 

  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                        44.75                        122.10 
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                        5.850                         7.695 
[1] "0.1 - 44.8 (5.8)"  "0.0 - 122.1 (7.7)"
[1] "hr=" "1.1"
D84V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 53(XQ11.2) MUTATED         1        1        0        0        10
  DEL PEAK 53(XQ11.2) WILD-TYPE       7        3        6        1        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 53(XQ11.2) MUTATED           6         5          1          4
  DEL PEAK 53(XQ11.2) WILD-TYPE        20        18         10          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 53(XQ11.2) MUTATED            0        0         0
  DEL PEAK 53(XQ11.2) WILD-TYPE          6        3         2
D84V3, multiclass
            clus
vv           DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             1                             3
  STAGE IB                             0                             6
  STAGE II                             0                             1
  STAGE IIA                           10                            25
  STAGE IIB                            6                            20
  STAGE III                            5                            18
  STAGE IIIA                           1                            10
  STAGE IIIB                           4                             4
  STAGE IIIC                           0                             6
  STAGE IV                             0                             3
  STAGE IVA                            0                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 53(XQ11.2) MUTATED       5  8 19  0
  DEL PEAK 53(XQ11.2) WILD-TYPE    21 25 55  4
D84V4, multiclass
       clus
vv      DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  T0+T1                           5                            21
  T2                              8                            25
  T3                             19                            55
  T4                              0                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 53(XQ11.2) MUTATED   15 12  5  0
  DEL PEAK 53(XQ11.2) WILD-TYPE 49 42  6  6
D84V5, multiclass
    clus
vv   DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  N0                          15                            49
  N1                          12                            42
  N2                           5                             6
  N3                           0                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 53(XQ11.2) MUTATED   26  0   0  4
  DEL PEAK 53(XQ11.2) WILD-TYPE 85  2   3 13
D84V6, multiclass
     clus
vv    DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  M0                           26                            85
  M1                            0                             2
  M1A                           0                             3
  MX                            4                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V7, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ11.2) MUTATED     6  29
  DEL PEAK 53(XQ11.2) WILD-TYPE  15 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ11.2) MUTATED      6   29
  DEL PEAK 53(XQ11.2) WILD-TYPE   15  100
        clus
vv       DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  FEMALE                           6                            15
  MALE                            29                           100
[1] 2 2
[1] FALSE
D84V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 53(XQ11.2) MUTATED      10                         1    18
  DEL PEAK 53(XQ11.2) WILD-TYPE    28                         1    75
D84V9, multiclass
                           clus
vv                          DEL PEAK 53(XQ11.2) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              18
                           clus
vv                          DEL PEAK 53(XQ11.2) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(85) Variable = DEL PEAK 54(XQ21.33) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 54(XQ21.33) MUTATED   24  7
  DEL PEAK 54(XQ21.33) WILD-TYPE 64 47
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                            31                            111 
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                             7                             47 
$`DEL PEAK 54(XQ21.33) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-JY-A6FH TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OJ 
       25.78         4.21        42.77        25.41         8.94         6.41 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NI 
        4.08         7.17         3.16         0.36         3.95        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-LN-A49M TCGA-LN-A49W TCGA-LN-A49Y 
       16.47        13.55        13.22         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-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        5.06         7.00         3.42         4.80         8.15         4.44 
TCGA-ZR-A9CJ 
       18.12 

$`DEL PEAK 54(XQ21.33) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         0.46         0.43       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       18.08        17.59         6.21         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        4.31         3.52         3.68         3.35        19.50         8.78 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         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-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.42        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.36         0.07        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.07         0.33         0.10         0.13         0.07         0.10 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.07         0.10         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
        0.20         5.16         3.78         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV 
        7.04        29.59         6.35        53.95         9.30         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 
       14.01         5.29         8.48        18.31         8.12        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.03         9.17        15.91 

  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                         42.77                         122.10 
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                          4.80                           8.12 
[1] "0.1 - 42.8 (4.8)"  "0.0 - 122.1 (8.1)"
[1] "hr=" "1.2"
D85V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 54(XQ21.33) MUTATED         1        3        1        1         9
  DEL PEAK 54(XQ21.33) WILD-TYPE       7        1        5        0        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 54(XQ21.33) MUTATED           3         7          0          0
  DEL PEAK 54(XQ21.33) WILD-TYPE        23        16         11          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 54(XQ21.33) MUTATED            1        0         0
  DEL PEAK 54(XQ21.33) WILD-TYPE          5        3         2
D85V3, multiclass
            clus
vv           DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              3                              1
  STAGE IB                              1                              5
  STAGE II                              1                              0
  STAGE IIA                             9                             26
  STAGE IIB                             3                             23
  STAGE III                             7                             16
  STAGE IIIA                            0                             11
  STAGE IIIB                            0                              8
  STAGE IIIC                            1                              5
  STAGE IV                              0                              3
  STAGE IVA                             0                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 54(XQ21.33) MUTATED       7  7 15  0
  DEL PEAK 54(XQ21.33) WILD-TYPE    19 26 59  4
D85V4, multiclass
       clus
vv      DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  T0+T1                            7                             19
  T2                               7                             26
  T3                              15                             59
  T4                               0                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 54(XQ21.33) MUTATED   17 10  1  1
  DEL PEAK 54(XQ21.33) WILD-TYPE 47 44 10  5
D85V5, multiclass
    clus
vv   DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  N0                           17                             47
  N1                           10                             44
  N2                            1                             10
  N3                            1                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 54(XQ21.33) MUTATED   23  0   0  5
  DEL PEAK 54(XQ21.33) WILD-TYPE 88  2   3 12
D85V6, multiclass
     clus
vv    DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  M0                            23                             88
  M1                             0                              2
  M1A                            0                              3
  MX                             5                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 54(XQ21.33) MUTATED     6  27
  DEL PEAK 54(XQ21.33) WILD-TYPE  15 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 54(XQ21.33) MUTATED      6   27
  DEL PEAK 54(XQ21.33) WILD-TYPE   15  102
        clus
vv       DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  FEMALE                            6                             15
  MALE                             27                            102
[1] 2 2
[1] FALSE
D85V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 54(XQ21.33) MUTATED      10                         1    18
  DEL PEAK 54(XQ21.33) WILD-TYPE    28                         1    75
D85V9, multiclass
                           clus
vv                          DEL PEAK 54(XQ21.33) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               18
                           clus
vv                          DEL PEAK 54(XQ21.33) WILD-TYPE
  ASIAN                                                 28
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
