
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/12/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/6158321/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/6154407/ESCA-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=ESCA-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=ESCA-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/6154407/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/6158321/transformed.cor.cli.txt"

nPatients in clinical file=22, in cluster file=73, common to both=22
[1] "Reduce the number of clustering variables from 67 to 65."
[1] 65 22
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            7                            15 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            7                            15 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           15                             7 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           15                             7 
[1] "AMP PEAK  3(2Q14.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                            6                            16 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                            6                            16 
[1] "AMP PEAK  4(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           19                             3 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           19                             3 
[1] "AMP PEAK  5(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                             9                             13 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                             9                             13 
[1] "AMP PEAK  6(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                            8                            14 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                            8                            14 
[1] "AMP PEAK  7(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          7                          15 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          7                          15 
[1] "AMP PEAK  8(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                           16                             6 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                           16                             6 
[1] "AMP PEAK  9(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                           15                             7 
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                           15                             7 
[1] "AMP PEAK 10(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                            13                              9 
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                            13                              9 
[1] "AMP PEAK 11(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            19                              3 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            19                              3 
[1] "AMP PEAK 12(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE 
                            4                            18 
  AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE 
                            4                            18 
[1] "AMP PEAK 14(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE 
                           5                           17 
  AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE 
                           5                           17 
[1] "AMP PEAK 15(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            11                             11 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            11                             11 
[1] "AMP PEAK 16(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                              9                              13 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                              9                              13 
[1] "AMP PEAK 17(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                             9                             13 
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                             9                             13 
[1] "AMP PEAK 18(14Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE 
                             7                             15 
  AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE 
                             7                             15 
[1] "AMP PEAK 19(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          11                           11 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          11                           11 
[1] "AMP PEAK 20(17Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE 
                            12                             10 
  AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE 
                            12                             10 
[1] "AMP PEAK 21(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE 
                              7                              15 
  AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE 
                              7                              15 
[1] "AMP PEAK 22(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE 
                             7                             15 
  AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE 
                             7                             15 
[1] "AMP PEAK 23(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                             3                             19 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                             3                             19 
[1] "AMP PEAK 24(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                           8                           14 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                           8                           14 
[1] "AMP PEAK 25(XP11.4) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                            4                            18 
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                            4                            18 
[1] "DEL PEAK  1(1P36.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            10                             12 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            10                             12 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           10                            12 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           10                            12 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          3                          19 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          3                          19 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            9                            13 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            9                            13 
[1] "DEL PEAK  5(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                            5                            17 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                            5                            17 
[1] "DEL PEAK  6(3P14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE 
                           15                             7 
  DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE 
                           15                             7 
[1] "DEL PEAK  7(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           16                             6 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           16                             6 
[1] "DEL PEAK  9(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                             3                             19 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                             3                             19 
[1] "DEL PEAK 10(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE 
                           14                             8 
  DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE 
                           14                             8 
[1] "DEL PEAK 11(4Q21.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE 
                            10                             12 
  DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE 
                            10                             12 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           12                            10 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           12                            10 
[1] "DEL PEAK 13(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           13                             9 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           13                             9 
[1] "DEL PEAK 14(5Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                           13                             9 
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                           13                             9 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                            9                            13 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                            9                            13 
[1] "DEL PEAK 16(6Q16.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE 
                            4                            18 
  DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE 
                            4                            18 
[1] "DEL PEAK 17(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            9                            13 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            9                            13 
[1] "DEL PEAK 18(7Q36.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                            9                            13 
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                            9                            13 
[1] "DEL PEAK 19(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                           12                            10 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                           12                            10 
[1] "DEL PEAK 20(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                           19                             3 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                           19                             3 
[1] "DEL PEAK 21(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                              6                              16 
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                              6                              16 
[1] "DEL PEAK 22(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              9                              13 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              9                              13 
[1] "DEL PEAK 23(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                             6                             16 
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                             6                             16 
[1] "DEL PEAK 24(11Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                             9                             13 
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                             9                             13 
[1] "DEL PEAK 25(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE 
                             6                             16 
  DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE 
                             6                             16 
[1] "DEL PEAK 26(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                             12                              10 
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                             12                              10 
[1] "DEL PEAK 27(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                            13                              9 
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                            13                              9 
[1] "DEL PEAK 28(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE 
                             5                             17 
  DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE 
                             5                             17 
[1] "DEL PEAK 29(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                            10                             12 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                            10                             12 
[1] "DEL PEAK 30(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE 
                             9                             13 
  DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE 
                             9                             13 
[1] "DEL PEAK 31(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                             4                             18 
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                             4                             18 
[1] "DEL PEAK 32(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE 
                            12                             10 
  DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE 
                            12                             10 
[1] "DEL PEAK 33(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                            12                             10 
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                            12                             10 
[1] "DEL PEAK 34(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            14                              8 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            14                              8 
[1] "DEL PEAK 35(19Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE 
                              6                              16 
  DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE 
                              6                              16 
[1] "DEL PEAK 36(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE 
                             3                             19 
  DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE 
                             3                             19 
[1] "DEL PEAK 37(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE 
                            15                              7 
  DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE 
                            15                              7 
[1] "DEL PEAK 38(21Q22.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE 
                             13                               9 
  DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE 
                             13                               9 
[1] "DEL PEAK 39(22Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE 
                            11                             11 
  DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE 
                            11                             11 
[1] "DEL PEAK 40(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                           12                            10 
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                           12                            10 
[1] "DEL PEAK 41(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE 
                           13                             9 
  DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE 
                           13                             9 
[1] "DEL PEAK 42(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE 
                             4                             18 
  DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE 
                             4                             18 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"          "VITALSTATUS"           "DAYSTODEATH"          
 [4] "DAYSTOLASTFOLLOWUP"    "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
 [7] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "DCCUPLOADDATE"        
[10] "GENDER"                "NUMBERPACKYEARSSMOKED" "GLEASON_SCORE"        
[13] "PSA_VALUE"             "DAYS_TO_PSA"           "BATCHNUMBER"          

Input Data has 15 rows and 22 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
          NA           NA           NA            1            8           16 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM 
          NA           NA           11          106          112          124 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
          NA          101           NA           NA          934          882 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
          NA           NA            4            2 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "NUMBERPACKYEARSSMOKED"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 22 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 4  7  9  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    4     7    11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 4  7  9  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    4     7    11 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
 8 10  3  1 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
    8    10     4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
 8 10  3  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
    8    10     4 
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=12, binary=FALSE, numeric=TRUE

Clustering(1) Variable = AMP PEAK  1(1P34.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1P34.2) MUTATED    2  3
  AMP PEAK  1(1P34.2) WILD-TYPE 10  3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            5                            13 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            3                             3 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-LN-A4A9 
        4.08        18.35         1.38         7.10         0.07 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE 
        0.03         0.26         0.53         0.79         0.36         3.48 
TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX 
        3.68         3.32         3.16        30.71        29.00         7.43 
TCGA-LN-A4A2 
        0.13 

  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 
                        18.35                         30.71 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                         4.08                          3.16 
[1] "0.1 - 18.4 (4.1)" "0.0 - 30.7 (3.2)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  1(1P34.2) MUTATED" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  1(1P34.2) MUTATED" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  1(1P34.2) MUTATED" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  1(1P34.2) MUTATED" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  1(1P34.2) MUTATED" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  1(1P34.2) MUTATED" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  1(1P34.2) MUTATED" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  1(1P34.2) MUTATED" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  1(1P34.2) MUTATED" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
[1] "hr=" "2"  
D1V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  1(1P34.2) MUTATED          1        0         1         3
  AMP PEAK  1(1P34.2) WILD-TYPE        1        1         2         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  1(1P34.2) MUTATED            2          0          0
  AMP PEAK  1(1P34.2) WILD-TYPE          3          3          1
D1V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  1(1P34.2) MUTATED    2  4     1
  AMP PEAK  1(1P34.2) WILD-TYPE  2  3    10
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T1                              2                             2
  T2                              4                             3
  T3+T4                           1                            10
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  1(1P34.2) MUTATED    3  4     0
  AMP PEAK  1(1P34.2) WILD-TYPE  5  6     4
D1V5, multiclass
       clus
vv      AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                              3                             5
  N1                              4                             6
  N2+N3                           0                             4
D1V6, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED    2  5
  AMP PEAK  1(1P34.2) WILD-TYPE  1 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      2    5
  AMP PEAK  1(1P34.2) WILD-TYPE    1   14
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                           2                             1
  MALE                             5                            14
D1V7, continuous

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  2(1Q21.3) MUTATED   8 4
  AMP PEAK  2(1Q21.3) WILD-TYPE 4 2
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           12                             6 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                            4                             2 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OM 
        0.03         0.26         0.53         0.79         0.36         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       18.35         1.38        30.71         7.43         0.13         0.07 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW 
        3.48         3.68         3.32         3.16        29.00         7.10 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.03                          3.16 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        30.71                         29.00 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.66                          3.58 
[1] "0.0 - 30.7 (0.7)" "3.2 - 29.0 (3.6)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  2(1Q21.3) MUTATED"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  2(1Q21.3) MUTATED"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  2(1Q21.3) WILD-TYPE"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"AMP PEAK  2(1Q21.3) WILD-TYPE"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  2(1Q21.3) MUTATED"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  2(1Q21.3) MUTATED"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  2(1Q21.3) MUTATED"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  2(1Q21.3) WILD-TYPE"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"AMP PEAK  2(1Q21.3) WILD-TYPE"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  2(1Q21.3) MUTATED"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  2(1Q21.3) MUTATED"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  2(1Q21.3) MUTATED"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  2(1Q21.3) WILD-TYPE"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  2(1Q21.3) MUTATED" "AMP PEAK  2(1Q21.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"AMP PEAK  2(1Q21.3) WILD-TYPE"   "AMP PEAK  2(1Q21.3) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  2(1Q21.3) MUTATED"   "AMP PEAK  2(1Q21.3) MUTATED" 
[1] "hr=" "1.6"
D2V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  2(1Q21.3) MUTATED          1        1         2         5
  AMP PEAK  2(1Q21.3) WILD-TYPE        1        0         1         2
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  2(1Q21.3) MUTATED            4          2          0
  AMP PEAK  2(1Q21.3) WILD-TYPE          1          1          1
D2V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  2(1Q21.3) MUTATED    2  6     7
  AMP PEAK  2(1Q21.3) WILD-TYPE  2  1     4
D2V4, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                              2                             2
  T2                              6                             1
  T3+T4                           7                             4
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  2(1Q21.3) MUTATED    5  8     2
  AMP PEAK  2(1Q21.3) WILD-TYPE  3  2     2
D2V5, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                              5                             3
  N1                              8                             2
  N2+N3                           2                             2
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED    2 13
  AMP PEAK  2(1Q21.3) WILD-TYPE  1  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      2   13
  AMP PEAK  2(1Q21.3) WILD-TYPE    1    6
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                           2                             1
  MALE                            13                             6
D2V7, continuous

Clustering(3) Variable = AMP PEAK  3(2Q14.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  3(2Q14.2) MUTATED   3 2
  AMP PEAK  3(2Q14.2) WILD-TYPE 9 4
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                            5                            13 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                            2                             4 
$`AMP PEAK  3(2Q14.2) MUTATED`
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-LN-A4A2 
        4.08         3.32         1.38         7.43         0.13 

$`AMP PEAK  3(2Q14.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE 
        0.03         0.26         0.53         0.79         0.36         3.48 
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        3.68        18.35         3.16        30.71        29.00         7.10 
TCGA-LN-A4A9 
        0.07 

  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                         0.13                          0.03 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                         7.43                         30.71 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                         3.32                          3.16 
[1] "0.1 - 7.4 (3.3)"  "0.0 - 30.7 (3.2)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  3(2Q14.2) WILD-TYPE"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"AMP PEAK  3(2Q14.2) WILD-TYPE"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  3(2Q14.2) MUTATED" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"AMP PEAK  3(2Q14.2) WILD-TYPE"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  3(2Q14.2) MUTATED" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  3(2Q14.2) WILD-TYPE"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"AMP PEAK  3(2Q14.2) WILD-TYPE"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  3(2Q14.2) MUTATED" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"AMP PEAK  3(2Q14.2) WILD-TYPE"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  3(2Q14.2) MUTATED" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  3(2Q14.2) WILD-TYPE"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"AMP PEAK  3(2Q14.2) WILD-TYPE"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  3(2Q14.2) MUTATED" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"AMP PEAK  3(2Q14.2) WILD-TYPE"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  3(2Q14.2) MUTATED" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
[1] "hr=" "1.7"
D3V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  3(2Q14.2) MUTATED          1        0         1         1
  AMP PEAK  3(2Q14.2) WILD-TYPE        1        1         2         6
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  3(2Q14.2) MUTATED            2          0          1
  AMP PEAK  3(2Q14.2) WILD-TYPE          3          3          0
D3V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  3(2Q14.2) MUTATED    1  2     3
  AMP PEAK  3(2Q14.2) WILD-TYPE  3  5     8
D3V4, multiclass
       clus
vv      AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  T1                              1                             3
  T2                              2                             5
  T3+T4                           3                             8
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  3(2Q14.2) MUTATED    2  3     1
  AMP PEAK  3(2Q14.2) WILD-TYPE  6  7     3
D3V5, multiclass
       clus
vv      AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  N0                              2                             6
  N1                              3                             7
  N2+N3                           1                             3
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(2Q14.2) MUTATED    1  5
  AMP PEAK  3(2Q14.2) WILD-TYPE  2 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q14.2) MUTATED      1    5
  AMP PEAK  3(2Q14.2) WILD-TYPE    2   14
        clus
vv       AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  FEMALE                           1                             2
  MALE                             5                            14
D3V7, continuous

Clustering(4) Variable = AMP PEAK  4(3Q26.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(3Q26.2) MUTATED   10  5
  AMP PEAK  4(3Q26.2) WILD-TYPE  2  1
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           15                             3 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                            5                             1 
$`AMP PEAK  4(3Q26.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE 
        0.03         0.26         0.53         0.79         0.36         3.48 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU 
        4.08        18.35         3.32         1.38         3.16        29.00 
TCGA-L5-A4OW TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.10         0.13         0.07 

$`AMP PEAK  4(3Q26.2) WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4OS TCGA-L5-A4OX 
        3.68        30.71         7.43 

  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                         0.03                          3.68 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                        29.00                         30.71 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                         1.38                          7.43 
[1] "0.0 - 29.0 (1.4)" "3.7 - 30.7 (7.4)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  4(3Q26.2) WILD-TYPE"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK  4(3Q26.2) WILD-TYPE"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  4(3Q26.2) WILD-TYPE"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK  4(3Q26.2) WILD-TYPE"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  4(3Q26.2) WILD-TYPE"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK  4(3Q26.2) WILD-TYPE"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
[1] "hr=" "2.7"
D4V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  4(3Q26.2) MUTATED          2        1         3         4
  AMP PEAK  4(3Q26.2) WILD-TYPE        0        0         0         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  4(3Q26.2) MUTATED            5          3          1
  AMP PEAK  4(3Q26.2) WILD-TYPE          0          0          0
D4V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  4(3Q26.2) MUTATED    3  5    11
  AMP PEAK  4(3Q26.2) WILD-TYPE  1  2     0
D4V4, multiclass
       clus
vv      AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  T1                              3                             1
  T2                              5                             2
  T3+T4                          11                             0
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  4(3Q26.2) MUTATED    8  7     4
  AMP PEAK  4(3Q26.2) WILD-TYPE  0  3     0
D4V5, multiclass
       clus
vv      AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  N0                              8                             0
  N1                              7                             3
  N2+N3                           4                             0
D4V6, binary
                               cls
clus                             0  1
  AMP PEAK  4(3Q26.2) MUTATED    2 17
  AMP PEAK  4(3Q26.2) WILD-TYPE  1  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      2   17
  AMP PEAK  4(3Q26.2) WILD-TYPE    1    2
        clus
vv       AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  FEMALE                           2                             1
  MALE                            17                             2
D4V7, continuous
[1] "Remove cluster labels:"        "AMP PEAK  4(3Q26.2) WILD-TYPE"
clus
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           13                             1 
                 TCGA-IG-A3Y9                  TCGA-IG-A3YA 
"AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) MUTATED" 
                 TCGA-IG-A4P3                  TCGA-IG-A50L 
"AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) MUTATED" 
                 TCGA-IG-A5B8                  TCGA-L5-A4OE 
"AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) MUTATED" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) MUTATED" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
"AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) MUTATED" 
                 TCGA-L5-A4OU                  TCGA-L5-A4OW 
"AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) MUTATED" 
                 TCGA-LN-A4A9 
"AMP PEAK  4(3Q26.2) MUTATED" 

Clustering(5) Variable = AMP PEAK  5(5P15.33) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                            0 1
  AMP PEAK  5(5P15.33) MUTATED   5 3
  AMP PEAK  5(5P15.33) WILD-TYPE 7 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                             8                             10 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                             3                              3 
$`AMP PEAK  5(5P15.33) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
        0.03         0.53         0.79         4.08         3.16        29.00 
TCGA-L5-A4OW TCGA-LN-A4A9 
        7.10         0.07 

$`AMP PEAK  5(5P15.33) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         0.36         3.48         3.68        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38        30.71         7.43         0.13 

  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                          0.03                           0.13 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                         29.00                          30.71 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                         1.975                          3.400 
[1] "0.0 - 29.0 (2.0)" "0.1 - 30.7 (3.4)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK  5(5P15.33) MUTATED"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK  5(5P15.33) MUTATED"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK  5(5P15.33) MUTATED"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK  5(5P15.33) WILD-TYPE"   "AMP PEAK  5(5P15.33) MUTATED" 
[1] "hr=" "1.8"
D5V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  5(5P15.33) MUTATED          2        1         2         2
  AMP PEAK  5(5P15.33) WILD-TYPE        0        0         1         5
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  5(5P15.33) MUTATED            2          0          0
  AMP PEAK  5(5P15.33) WILD-TYPE          3          3          1
D5V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK  5(5P15.33) MUTATED    2  3     4
  AMP PEAK  5(5P15.33) WILD-TYPE  2  4     7
D5V4, multiclass
       clus
vv      AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  T1                               2                              2
  T2                               3                              4
  T3+T4                            4                              7
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK  5(5P15.33) MUTATED    5  4     0
  AMP PEAK  5(5P15.33) WILD-TYPE  3  6     4
D5V5, multiclass
       clus
vv      AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  N0                               5                              3
  N1                               4                              6
  N2+N3                            0                              4
D5V6, binary
                                cls
clus                              0  1
  AMP PEAK  5(5P15.33) MUTATED    2  7
  AMP PEAK  5(5P15.33) WILD-TYPE  1 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED      2    7
  AMP PEAK  5(5P15.33) WILD-TYPE    1   12
        clus
vv       AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  FEMALE                            2                              1
  MALE                              7                             12
D5V7, continuous

Clustering(6) Variable = AMP PEAK  6(6P21.1) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  6(6P21.1) MUTATED   5 3
  AMP PEAK  6(6P21.1) WILD-TYPE 7 3
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                            8                            10 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                            3                             3 
$`AMP PEAK  6(6P21.1) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
        0.26         4.08        18.35         1.38        30.71         7.10 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

$`AMP PEAK  6(6P21.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.53         0.79         0.36         3.48         3.68 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         3.16        29.00         7.43 

  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                        30.71                         29.00 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                         2.73                          3.24 
[1] "0.1 - 30.7 (2.7)" "0.0 - 29.0 (3.2)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK  6(6P21.1) WILD-TYPE" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  6(6P21.1) WILD-TYPE" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  6(6P21.1) MUTATED"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK  6(6P21.1) WILD-TYPE" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  6(6P21.1) WILD-TYPE" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  6(6P21.1) MUTATED"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK  6(6P21.1) WILD-TYPE" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  6(6P21.1) WILD-TYPE" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  6(6P21.1) MUTATED" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  6(6P21.1) MUTATED"   "AMP PEAK  6(6P21.1) MUTATED" 
[1] "hr=" "1"  
D6V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  6(6P21.1) MUTATED          1        0         2         3
  AMP PEAK  6(6P21.1) WILD-TYPE        1        1         1         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  6(6P21.1) MUTATED            1          1          0
  AMP PEAK  6(6P21.1) WILD-TYPE          4          2          1
D6V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  6(6P21.1) MUTATED    2  4     2
  AMP PEAK  6(6P21.1) WILD-TYPE  2  3     9
D6V4, multiclass
       clus
vv      AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  T1                              2                             2
  T2                              4                             3
  T3+T4                           2                             9
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  6(6P21.1) MUTATED    3  4     1
  AMP PEAK  6(6P21.1) WILD-TYPE  5  6     3
D6V5, multiclass
       clus
vv      AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  N0                              3                             5
  N1                              4                             6
  N2+N3                           1                             3
D6V6, binary
                               cls
clus                             0  1
  AMP PEAK  6(6P21.1) MUTATED    3  5
  AMP PEAK  6(6P21.1) WILD-TYPE  0 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P21.1) MUTATED      3    5
  AMP PEAK  6(6P21.1) WILD-TYPE    0   14
        clus
vv       AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  FEMALE                           3                             0
  MALE                             5                            14
D6V7, continuous

Clustering(7) Variable = AMP PEAK  7(6Q12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  7(6Q12) MUTATED    2  4
  AMP PEAK  7(6Q12) WILD-TYPE 10  2
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          6                          12 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          4                           2 
$`AMP PEAK  7(6Q12) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        0.26        18.35         1.38         7.10         7.43         0.07 

$`AMP PEAK  7(6Q12) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.53         0.79         0.36         3.48         3.68 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-LN-A4A2 
        4.08         3.32         3.16        30.71        29.00         0.13 

  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                       0.07                        0.03 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                      18.35                       30.71 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                       4.24                        3.24 
[1] "0.1 - 18.4 (4.2)" "0.0 - 30.7 (3.2)"
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-IG-A50L                  TCGA-IG-A5B8 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-IG-A625                  TCGA-L5-A4OE 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OF                  TCGA-L5-A4OM 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4ON                  TCGA-L5-A4OO 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OQ                  TCGA-L5-A4OR 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OS                  TCGA-L5-A4OU 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OW                  TCGA-L5-A4OX 
  "AMP PEAK  7(6Q12) MUTATED"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-LN-A4A2                  TCGA-LN-A4A9 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-IG-A50L                  TCGA-IG-A5B8 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-IG-A625                  TCGA-L5-A4OE 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OF                  TCGA-L5-A4OM 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4ON                  TCGA-L5-A4OO 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OQ                  TCGA-L5-A4OR 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OS                  TCGA-L5-A4OU 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OW                  TCGA-L5-A4OX 
  "AMP PEAK  7(6Q12) MUTATED"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-LN-A4A2                  TCGA-LN-A4A9 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-IG-A50L                  TCGA-IG-A5B8 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-IG-A625                  TCGA-L5-A4OE 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OF                  TCGA-L5-A4OM 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4ON                  TCGA-L5-A4OO 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OQ                  TCGA-L5-A4OR 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OS                  TCGA-L5-A4OU 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OW                  TCGA-L5-A4OX 
  "AMP PEAK  7(6Q12) MUTATED"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-LN-A4A2                  TCGA-LN-A4A9 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
[1] "hr=" "3.1"
D7V2, continuous
                             vv
clus                          STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  7(6Q12) MUTATED          0        0         1         3          2
  AMP PEAK  7(6Q12) WILD-TYPE        2        1         2         4          3
                             vv
clus                          STAGE IIIB STAGE IIIC
  AMP PEAK  7(6Q12) MUTATED            1          0
  AMP PEAK  7(6Q12) WILD-TYPE          2          1
D7V3, multiclass
                             vv
clus                          T1 T2 T3+T4
  AMP PEAK  7(6Q12) MUTATED    1  4     2
  AMP PEAK  7(6Q12) WILD-TYPE  3  3     9
D7V4, multiclass
       clus
vv      AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  T1                            1                           3
  T2                            4                           3
  T3+T4                         2                           9
                             vv
clus                          N0 N1 N2+N3
  AMP PEAK  7(6Q12) MUTATED    2  4     1
  AMP PEAK  7(6Q12) WILD-TYPE  6  6     3
D7V5, multiclass
       clus
vv      AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  N0                            2                           6
  N1                            4                           6
  N2+N3                         1                           3
D7V6, binary
                             cls
clus                           0  1
  AMP PEAK  7(6Q12) MUTATED    1  6
  AMP PEAK  7(6Q12) WILD-TYPE  2 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED      1    6
  AMP PEAK  7(6Q12) WILD-TYPE    2   13
        clus
vv       AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  FEMALE                         1                           2
  MALE                           6                          13
D7V7, continuous

Clustering(8) Variable = AMP PEAK  8(7P11.2) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  8(7P11.2) MUTATED   9 5
  AMP PEAK  8(7P11.2) WILD-TYPE 3 1
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                           14                             4 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                            5                             1 
$`AMP PEAK  8(7P11.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM 
        0.03         0.53         0.79         3.48         3.68         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         3.32         1.38         3.16        30.71        29.00 
TCGA-L5-A4OW TCGA-LN-A4A2 
        7.10         0.13 

$`AMP PEAK  8(7P11.2) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A625 TCGA-L5-A4OX TCGA-LN-A4A9 
        0.26         0.36         7.43         0.07 

  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                        30.71                          7.43 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                         3.40                          0.31 
[1] "0.0 - 30.7 (3.4)" "0.1 - 7.4 (0.3)" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  8(7P11.2) MUTATED" "AMP PEAK  8(7P11.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  8(7P11.2) WILD-TYPE"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  8(7P11.2) MUTATED" "AMP PEAK  8(7P11.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  8(7P11.2) MUTATED" "AMP PEAK  8(7P11.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  8(7P11.2) MUTATED" "AMP PEAK  8(7P11.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  8(7P11.2) WILD-TYPE"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  8(7P11.2) MUTATED" "AMP PEAK  8(7P11.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  8(7P11.2) MUTATED" "AMP PEAK  8(7P11.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  8(7P11.2) MUTATED" "AMP PEAK  8(7P11.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  8(7P11.2) WILD-TYPE"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  8(7P11.2) MUTATED" "AMP PEAK  8(7P11.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  8(7P11.2) MUTATED" "AMP PEAK  8(7P11.2) WILD-TYPE" 
[1] "hr=" "1.5"
D8V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  8(7P11.2) MUTATED          2        1         2         6
  AMP PEAK  8(7P11.2) WILD-TYPE        0        0         1         1
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  8(7P11.2) MUTATED            3          1          1
  AMP PEAK  8(7P11.2) WILD-TYPE          2          2          0
D8V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  8(7P11.2) MUTATED    4  5     7
  AMP PEAK  8(7P11.2) WILD-TYPE  0  2     4
D8V4, multiclass
       clus
vv      AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  T1                              4                             0
  T2                              5                             2
  T3+T4                           7                             4
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  8(7P11.2) MUTATED    6  8     2
  AMP PEAK  8(7P11.2) WILD-TYPE  2  2     2
D8V5, multiclass
       clus
vv      AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  N0                              6                             2
  N1                              8                             2
  N2+N3                           2                             2
D8V6, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P11.2) MUTATED    3 13
  AMP PEAK  8(7P11.2) WILD-TYPE  0  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED      3   13
  AMP PEAK  8(7P11.2) WILD-TYPE    0    6
        clus
vv       AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  FEMALE                           3                             0
  MALE                            13                             6
D8V7, continuous

Clustering(9) Variable = AMP PEAK  9(7Q21.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  9(7Q21.2) MUTATED   9 4
  AMP PEAK  9(7Q21.2) WILD-TYPE 3 2
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                           13                             5 
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                            4                             2 
$`AMP PEAK  9(7Q21.2) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         0.53         3.48         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A2 
        1.38         3.16        30.71        29.00         7.10         0.13 
TCGA-LN-A4A9 
        0.07 

$`AMP PEAK  9(7Q21.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OX 
        0.03         0.79         0.36         3.68         7.43 

  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                        30.71                          7.43 
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                         3.32                          0.79 
[1] "0.1 - 30.7 (3.3)" "0.0 - 7.4 (0.8)" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  9(7Q21.2) MUTATED" "AMP PEAK  9(7Q21.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  9(7Q21.2) MUTATED" "AMP PEAK  9(7Q21.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  9(7Q21.2) MUTATED" "AMP PEAK  9(7Q21.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  9(7Q21.2) MUTATED" "AMP PEAK  9(7Q21.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "AMP PEAK  9(7Q21.2) MUTATED" "AMP PEAK  9(7Q21.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK  9(7Q21.2) MUTATED" "AMP PEAK  9(7Q21.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
[1] "hr=" "2.4"
D9V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  9(7Q21.2) MUTATED          2        0         3         4
  AMP PEAK  9(7Q21.2) WILD-TYPE        0        1         0         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  9(7Q21.2) MUTATED            3          2          1
  AMP PEAK  9(7Q21.2) WILD-TYPE          2          1          0
D9V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  9(7Q21.2) MUTATED    3  5     7
  AMP PEAK  9(7Q21.2) WILD-TYPE  1  2     4
D9V4, multiclass
       clus
vv      AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE
  T1                              3                             1
  T2                              5                             2
  T3+T4                           7                             4
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK  9(7Q21.2) MUTATED    5  7     3
  AMP PEAK  9(7Q21.2) WILD-TYPE  3  3     1
D9V5, multiclass
       clus
vv      AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE
  N0                              5                             3
  N1                              7                             3
  N2+N3                           3                             1
D9V6, binary
                               cls
clus                             0  1
  AMP PEAK  9(7Q21.2) MUTATED    3 12
  AMP PEAK  9(7Q21.2) WILD-TYPE  0  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.2) MUTATED      3   12
  AMP PEAK  9(7Q21.2) WILD-TYPE    0    7
        clus
vv       AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE
  FEMALE                           3                             0
  MALE                            12                             7
D9V7, continuous

Clustering(10) Variable = AMP PEAK 10(8P11.21) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 10(8P11.21) MUTATED   7 4
  AMP PEAK 10(8P11.21) WILD-TYPE 5 2
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                            11                              7 
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                             4                              2 
$`AMP PEAK 10(8P11.21) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         0.36         3.68         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        3.32         3.16         7.10         7.43         0.07 

$`AMP PEAK 10(8P11.21) WILD-TYPE`
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        0.53         0.79         3.48         1.38        30.71        29.00 
TCGA-LN-A4A2 
        0.13 

  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                          0.03                           0.13 
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                         18.35                          30.71 
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                          3.32                           1.38 
[1] "0.0 - 18.4 (3.3)" "0.1 - 30.7 (1.4)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 10(8P11.21) WILD-TYPE" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 10(8P11.21) WILD-TYPE" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 10(8P11.21) WILD-TYPE" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 10(8P11.21) WILD-TYPE" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 10(8P11.21) WILD-TYPE" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 10(8P11.21) WILD-TYPE" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
[1] "hr=" "1.6"
D10V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 10(8P11.21) MUTATED          2        0         1         6
  AMP PEAK 10(8P11.21) WILD-TYPE        0        1         2         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 10(8P11.21) MUTATED            1          2          1
  AMP PEAK 10(8P11.21) WILD-TYPE          4          1          0
D10V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 10(8P11.21) MUTATED    4  5     4
  AMP PEAK 10(8P11.21) WILD-TYPE  0  2     7
D10V4, multiclass
       clus
vv      AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE
  T1                               4                              0
  T2                               5                              2
  T3+T4                            4                              7
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 10(8P11.21) MUTATED    4  6     3
  AMP PEAK 10(8P11.21) WILD-TYPE  4  4     1
D10V5, multiclass
       clus
vv      AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE
  N0                               4                              4
  N1                               6                              4
  N2+N3                            3                              1
D10V6, binary
                                cls
clus                              0  1
  AMP PEAK 10(8P11.21) MUTATED    2 11
  AMP PEAK 10(8P11.21) WILD-TYPE  1  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.21) MUTATED      2   11
  AMP PEAK 10(8P11.21) WILD-TYPE    1    8
        clus
vv       AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE
  FEMALE                            2                              1
  MALE                             11                              8
D10V7, continuous

Clustering(11) Variable = AMP PEAK 11(8Q24.21) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 11(8Q24.21) MUTATED   9 6
  AMP PEAK 11(8Q24.21) WILD-TYPE 3 0
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            15                              3 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                             6                              0 
$`AMP PEAK 11(8Q24.21) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OM 
        0.26         0.53         0.79         0.36         3.48         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
       18.35         3.32         1.38         3.16        30.71         7.10 
TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.43         0.13         0.07 

$`AMP PEAK 11(8Q24.21) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OU 
        0.03         3.68        29.00 

  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                         30.71                          29.00 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                          3.16                           3.68 
[1] "0.1 - 30.7 (3.2)" "0.0 - 29.0 (3.7)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
[1] "hr="     "7.6e+08"
D11V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 11(8Q24.21) MUTATED          2        1         2         5
  AMP PEAK 11(8Q24.21) WILD-TYPE        0        0         1         2
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 11(8Q24.21) MUTATED            5          3          1
  AMP PEAK 11(8Q24.21) WILD-TYPE          0          0          0
D11V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 11(8Q24.21) MUTATED    3  6    10
  AMP PEAK 11(8Q24.21) WILD-TYPE  1  1     1
D11V4, multiclass
       clus
vv      AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  T1                               3                              1
  T2                               6                              1
  T3+T4                           10                              1
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 11(8Q24.21) MUTATED    7  8     4
  AMP PEAK 11(8Q24.21) WILD-TYPE  1  2     0
D11V5, multiclass
       clus
vv      AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  N0                               7                              1
  N1                               8                              2
  N2+N3                            4                              0
D11V6, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED    3 16
  AMP PEAK 11(8Q24.21) WILD-TYPE  0  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED      3   16
  AMP PEAK 11(8Q24.21) WILD-TYPE    0    3
        clus
vv       AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  FEMALE                            3                              0
  MALE                             16                              3
D11V7, continuous
[1] "Remove cluster labels:"         "AMP PEAK 11(8Q24.21) WILD-TYPE"
clus
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            12                              2 
                  TCGA-IG-A3Y9                   TCGA-IG-A3YA 
"AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) MUTATED" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
"AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) MUTATED" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OM 
"AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) MUTATED" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
"AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) MUTATED" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OW 
"AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) MUTATED" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A9 
"AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) MUTATED" 

Clustering(12) Variable = AMP PEAK 12(9P13.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 12(9P13.3) MUTATED    2  2
  AMP PEAK 12(9P13.3) WILD-TYPE 10  4
  AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE 
                            4                            14 
  AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE 
                            2                             4 
$`AMP PEAK 12(9P13.3) MUTATED`
TCGA-IG-A625 TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU 
        0.36        18.35         3.16        29.00 

$`AMP PEAK 12(9P13.3) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.26         0.53         0.79         3.48         3.68 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        4.08         3.32         1.38        30.71         7.10         7.43 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE 
                         0.36                          0.03 
  AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE 
                        29.00                         30.71 
  AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE 
                       10.755                         2.350 
[1] "0.4 - 29.0 (10.8)" "0.0 - 30.7 (2.3)" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "AMP PEAK 12(9P13.3) MUTATED" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK 12(9P13.3) MUTATED" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"AMP PEAK 12(9P13.3) WILD-TYPE"   "AMP PEAK 12(9P13.3) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK 12(9P13.3) WILD-TYPE"   "AMP PEAK 12(9P13.3) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "AMP PEAK 12(9P13.3) MUTATED" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK 12(9P13.3) MUTATED" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"AMP PEAK 12(9P13.3) WILD-TYPE"   "AMP PEAK 12(9P13.3) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK 12(9P13.3) WILD-TYPE"   "AMP PEAK 12(9P13.3) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "AMP PEAK 12(9P13.3) MUTATED" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "AMP PEAK 12(9P13.3) MUTATED" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"AMP PEAK 12(9P13.3) WILD-TYPE"   "AMP PEAK 12(9P13.3) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK 12(9P13.3) WILD-TYPE"   "AMP PEAK 12(9P13.3) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
[1] "hr=" "1.4"
D12V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 12(9P13.3) MUTATED          1        0         1         1
  AMP PEAK 12(9P13.3) WILD-TYPE        1        1         2         6
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 12(9P13.3) MUTATED            0          1          0
  AMP PEAK 12(9P13.3) WILD-TYPE          5          2          1
D12V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK 12(9P13.3) MUTATED    2  0     2
  AMP PEAK 12(9P13.3) WILD-TYPE  2  7     9
D12V4, multiclass
       clus
vv      AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE
  T1                              2                             2
  T2                              0                             7
  T3+T4                           2                             9
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK 12(9P13.3) MUTATED    2  1     1
  AMP PEAK 12(9P13.3) WILD-TYPE  6  9     3
D12V5, multiclass
       clus
vv      AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE
  N0                              2                             6
  N1                              1                             9
  N2+N3                           1                             3
D12V6, binary
                               cls
clus                             0  1
  AMP PEAK 12(9P13.3) MUTATED    0  4
  AMP PEAK 12(9P13.3) WILD-TYPE  3 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P13.3) MUTATED      0    4
  AMP PEAK 12(9P13.3) WILD-TYPE    3   15
        clus
vv       AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE
  FEMALE                           0                             3
  MALE                             4                            15
D12V7, continuous
[1] "Remove cluster labels:"      "AMP PEAK 12(9P13.3) MUTATED"
clus
  AMP PEAK 12(9P13.3) MUTATED AMP PEAK 12(9P13.3) WILD-TYPE 
                            2                            12 
                   TCGA-IG-A3Y9                    TCGA-IG-A3YA 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A50L 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-IG-A5B8                    TCGA-L5-A4OE 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4OO 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OW 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A9 
"AMP PEAK 12(9P13.3) WILD-TYPE" "AMP PEAK 12(9P13.3) WILD-TYPE" 

Clustering(13) Variable = AMP PEAK 14(11P13) MUTATION ANALYSIS
D13V1, survival
                              sevent
clus2                          0 1
  AMP PEAK 14(11P13) MUTATED   4 1
  AMP PEAK 14(11P13) WILD-TYPE 8 5
  AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE 
                           5                           13 
  AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE 
                           1                            5 
$`AMP PEAK 14(11P13) MUTATED`
TCGA-IG-A50L TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OU 
        0.53         3.48         4.08        18.35        29.00 

$`AMP PEAK 14(11P13) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OO 
        0.03         0.26         0.79         0.36         3.68         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38         3.16        30.71         7.10         7.43         0.13 
TCGA-LN-A4A9 
        0.07 

  AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE 
                        0.53                         0.03 
  AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE 
                       29.00                        30.71 
  AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE 
                        4.08                         1.38 
[1] "0.5 - 29.0 (4.1)" "0.0 - 30.7 (1.4)"
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
  "AMP PEAK 14(11P13) MUTATED" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-IG-A625                   TCGA-L5-A4OE 
"AMP PEAK 14(11P13) WILD-TYPE"   "AMP PEAK 14(11P13) MUTATED" 
                  TCGA-L5-A4OF                   TCGA-L5-A4OM 
"AMP PEAK 14(11P13) WILD-TYPE"   "AMP PEAK 14(11P13) MUTATED" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
  "AMP PEAK 14(11P13) MUTATED" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OR 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-L5-A4OS                   TCGA-L5-A4OU 
"AMP PEAK 14(11P13) WILD-TYPE"   "AMP PEAK 14(11P13) MUTATED" 
                  TCGA-L5-A4OW                   TCGA-L5-A4OX 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-LN-A4A2                   TCGA-LN-A4A9 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
  "AMP PEAK 14(11P13) MUTATED" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-IG-A625                   TCGA-L5-A4OE 
"AMP PEAK 14(11P13) WILD-TYPE"   "AMP PEAK 14(11P13) MUTATED" 
                  TCGA-L5-A4OF                   TCGA-L5-A4OM 
"AMP PEAK 14(11P13) WILD-TYPE"   "AMP PEAK 14(11P13) MUTATED" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
  "AMP PEAK 14(11P13) MUTATED" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OR 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-L5-A4OS                   TCGA-L5-A4OU 
"AMP PEAK 14(11P13) WILD-TYPE"   "AMP PEAK 14(11P13) MUTATED" 
                  TCGA-L5-A4OW                   TCGA-L5-A4OX 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-LN-A4A2                   TCGA-LN-A4A9 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
  "AMP PEAK 14(11P13) MUTATED" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-IG-A625                   TCGA-L5-A4OE 
"AMP PEAK 14(11P13) WILD-TYPE"   "AMP PEAK 14(11P13) MUTATED" 
                  TCGA-L5-A4OF                   TCGA-L5-A4OM 
"AMP PEAK 14(11P13) WILD-TYPE"   "AMP PEAK 14(11P13) MUTATED" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
  "AMP PEAK 14(11P13) MUTATED" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OR 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-L5-A4OS                   TCGA-L5-A4OU 
"AMP PEAK 14(11P13) WILD-TYPE"   "AMP PEAK 14(11P13) MUTATED" 
                  TCGA-L5-A4OW                   TCGA-L5-A4OX 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
                  TCGA-LN-A4A2                   TCGA-LN-A4A9 
"AMP PEAK 14(11P13) WILD-TYPE" "AMP PEAK 14(11P13) WILD-TYPE" 
[1] "hr=" "4.3"
D13V2, continuous
                              vv
clus                           STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 14(11P13) MUTATED          1        0         1         1          1
  AMP PEAK 14(11P13) WILD-TYPE        1        1         2         6          4
                              vv
clus                           STAGE IIIB STAGE IIIC
  AMP PEAK 14(11P13) MUTATED            1          0
  AMP PEAK 14(11P13) WILD-TYPE          2          1
D13V3, multiclass
                              vv
clus                           T1 T2 T3+T4
  AMP PEAK 14(11P13) MUTATED    2  0     3
  AMP PEAK 14(11P13) WILD-TYPE  2  7     8
D13V4, multiclass
       clus
vv      AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE
  T1                             2                            2
  T2                             0                            7
  T3+T4                          3                            8
                              vv
clus                           N0 N1 N2+N3
  AMP PEAK 14(11P13) MUTATED    2  2     1
  AMP PEAK 14(11P13) WILD-TYPE  6  8     3
D13V5, multiclass
       clus
vv      AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE
  N0                             2                            6
  N1                             2                            8
  N2+N3                          1                            3
D13V6, binary
                              cls
clus                            0  1
  AMP PEAK 14(11P13) MUTATED    1  4
  AMP PEAK 14(11P13) WILD-TYPE  2 15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(11P13) MUTATED      1    4
  AMP PEAK 14(11P13) WILD-TYPE    2   15
        clus
vv       AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE
  FEMALE                          1                            2
  MALE                            4                           15
D13V7, continuous

Clustering(14) Variable = AMP PEAK 15(11Q13.3) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 15(11Q13.3) MUTATED   7 1
  AMP PEAK 15(11Q13.3) WILD-TYPE 5 5
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                             8                             10 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                             1                              5 
$`AMP PEAK 15(11Q13.3) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.03         3.48         3.68         4.08         1.38        30.71 
TCGA-L5-A4OU TCGA-LN-A4A2 
       29.00         0.13 

$`AMP PEAK 15(11Q13.3) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         0.53         0.79         0.36        18.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        3.16         7.10         7.43         0.07 

  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                         30.71                          18.35 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                         3.580                          1.975 
[1] "0.0 - 30.7 (3.6)" "0.1 - 18.4 (2.0)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 15(11Q13.3) MUTATED" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "AMP PEAK 15(11Q13.3) MUTATED"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "AMP PEAK 15(11Q13.3) MUTATED" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "AMP PEAK 15(11Q13.3) MUTATED"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "AMP PEAK 15(11Q13.3) MUTATED" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 15(11Q13.3) MUTATED" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "AMP PEAK 15(11Q13.3) MUTATED"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "AMP PEAK 15(11Q13.3) MUTATED" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "AMP PEAK 15(11Q13.3) MUTATED"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "AMP PEAK 15(11Q13.3) MUTATED" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 15(11Q13.3) MUTATED" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "AMP PEAK 15(11Q13.3) MUTATED"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "AMP PEAK 15(11Q13.3) MUTATED" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "AMP PEAK 15(11Q13.3) MUTATED"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "AMP PEAK 15(11Q13.3) MUTATED" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
[1] "hr=" "5.6"
D14V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 15(11Q13.3) MUTATED          1        0         2         4
  AMP PEAK 15(11Q13.3) WILD-TYPE        1        1         1         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 15(11Q13.3) MUTATED            3          1          0
  AMP PEAK 15(11Q13.3) WILD-TYPE          2          2          1
D14V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 15(11Q13.3) MUTATED    2  4     5
  AMP PEAK 15(11Q13.3) WILD-TYPE  2  3     6
D14V4, multiclass
       clus
vv      AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  T1                               2                              2
  T2                               4                              3
  T3+T4                            5                              6
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 15(11Q13.3) MUTATED    5  5     1
  AMP PEAK 15(11Q13.3) WILD-TYPE  3  5     3
D14V5, multiclass
       clus
vv      AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  N0                               5                              3
  N1                               5                              5
  N2+N3                            1                              3
D14V6, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.3) MUTATED    2  9
  AMP PEAK 15(11Q13.3) WILD-TYPE  1 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      2    9
  AMP PEAK 15(11Q13.3) WILD-TYPE    1   10
        clus
vv       AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  FEMALE                            2                              1
  MALE                              9                             10
D14V7, continuous

Clustering(15) Variable = AMP PEAK 16(12P13.33) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                             0 1
  AMP PEAK 16(12P13.33) MUTATED   6 1
  AMP PEAK 16(12P13.33) WILD-TYPE 6 5
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                              7                              11 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                              1                               5 
$`AMP PEAK 16(12P13.33) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         0.53         3.48         4.08         3.32         3.16 
TCGA-LN-A4A2 
        0.13 

$`AMP PEAK 16(12P13.33) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.26         0.79         0.36         3.68        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
       30.71        29.00         7.10         7.43         0.07 

  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                           0.03                            0.07 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                           4.08                           30.71 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                           3.16                            3.68 
[1] "0.0 - 4.1 (3.2)"  "0.1 - 30.7 (3.7)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "AMP PEAK 16(12P13.33) MUTATED" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "AMP PEAK 16(12P13.33) MUTATED" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"AMP PEAK 16(12P13.33) WILD-TYPE" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"AMP PEAK 16(12P13.33) WILD-TYPE" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "AMP PEAK 16(12P13.33) MUTATED" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "AMP PEAK 16(12P13.33) MUTATED" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "AMP PEAK 16(12P13.33) MUTATED" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"AMP PEAK 16(12P13.33) WILD-TYPE" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"AMP PEAK 16(12P13.33) WILD-TYPE" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "AMP PEAK 16(12P13.33) MUTATED" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "AMP PEAK 16(12P13.33) MUTATED" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "AMP PEAK 16(12P13.33) MUTATED" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"AMP PEAK 16(12P13.33) WILD-TYPE"   "AMP PEAK 16(12P13.33) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"AMP PEAK 16(12P13.33) WILD-TYPE" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"AMP PEAK 16(12P13.33) WILD-TYPE" "AMP PEAK 16(12P13.33) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "AMP PEAK 16(12P13.33) MUTATED" "AMP PEAK 16(12P13.33) WILD-TYPE" 
[1] "hr=" "1.2"
D15V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 16(12P13.33) MUTATED          2        0         1         1
  AMP PEAK 16(12P13.33) WILD-TYPE        0        1         2         6
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 16(12P13.33) MUTATED            3          1          1
  AMP PEAK 16(12P13.33) WILD-TYPE          2          2          0
D15V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  AMP PEAK 16(12P13.33) MUTATED    2  1     6
  AMP PEAK 16(12P13.33) WILD-TYPE  2  6     5
D15V4, multiclass
       clus
vv      AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  T1                                2                               2
  T2                                1                               6
  T3+T4                             6                               5
                                 vv
clus                              N0 N1 N2+N3
  AMP PEAK 16(12P13.33) MUTATED    4  3     2
  AMP PEAK 16(12P13.33) WILD-TYPE  4  7     2
D15V5, multiclass
       clus
vv      AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  N0                                4                               4
  N1                                3                               7
  N2+N3                             2                               2
D15V6, binary
                                 cls
clus                               0  1
  AMP PEAK 16(12P13.33) MUTATED    1  8
  AMP PEAK 16(12P13.33) WILD-TYPE  2 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED      1    8
  AMP PEAK 16(12P13.33) WILD-TYPE    2   11
        clus
vv       AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  FEMALE                             1                               2
  MALE                               8                              11
D15V7, continuous

Clustering(16) Variable = AMP PEAK 17(12P12.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 17(12P12.1) MUTATED   7 1
  AMP PEAK 17(12P12.1) WILD-TYPE 5 5
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                             8                             10 
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                             1                              5 
$`AMP PEAK 17(12P12.1) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         0.53         3.48         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OU 
        3.32        29.00 

$`AMP PEAK 17(12P12.1) WILD-TYPE`
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        0.79         0.36         3.68         1.38         3.16        30.71 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.10         7.43         0.13         0.07 

  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                         29.00                          30.71 
  AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE 
                          3.40                           2.27 
[1] "0.0 - 29.0 (3.4)" "0.1 - 30.7 (2.3)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 17(12P12.1) MUTATED"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK 17(12P12.1) MUTATED" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 17(12P12.1) WILD-TYPE"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 17(12P12.1) WILD-TYPE"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 17(12P12.1) MUTATED"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 17(12P12.1) WILD-TYPE" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 17(12P12.1) WILD-TYPE"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 17(12P12.1) WILD-TYPE" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 17(12P12.1) WILD-TYPE" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 17(12P12.1) MUTATED"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK 17(12P12.1) MUTATED" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 17(12P12.1) WILD-TYPE"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 17(12P12.1) WILD-TYPE"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 17(12P12.1) MUTATED"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 17(12P12.1) WILD-TYPE" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 17(12P12.1) WILD-TYPE"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 17(12P12.1) WILD-TYPE" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 17(12P12.1) WILD-TYPE" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 17(12P12.1) MUTATED"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK 17(12P12.1) MUTATED" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 17(12P12.1) WILD-TYPE"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 17(12P12.1) WILD-TYPE"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 17(12P12.1) MUTATED"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 17(12P12.1) WILD-TYPE" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 17(12P12.1) WILD-TYPE"   "AMP PEAK 17(12P12.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 17(12P12.1) WILD-TYPE" "AMP PEAK 17(12P12.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 17(12P12.1) WILD-TYPE" "AMP PEAK 17(12P12.1) WILD-TYPE" 
[1] "hr=" "5"  
D16V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 17(12P12.1) MUTATED          1        0         1         2
  AMP PEAK 17(12P12.1) WILD-TYPE        1        1         2         5
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 17(12P12.1) MUTATED            2          2          1
  AMP PEAK 17(12P12.1) WILD-TYPE          3          1          0
D16V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 17(12P12.1) MUTATED    2  1     6
  AMP PEAK 17(12P12.1) WILD-TYPE  2  6     5
D16V4, multiclass
       clus
vv      AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  T1                               2                              2
  T2                               1                              6
  T3+T4                            6                              5
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 17(12P12.1) MUTATED    2  4     3
  AMP PEAK 17(12P12.1) WILD-TYPE  6  6     1
D16V5, multiclass
       clus
vv      AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  N0                               2                              6
  N1                               4                              6
  N2+N3                            3                              1
D16V6, binary
                                cls
clus                              0  1
  AMP PEAK 17(12P12.1) MUTATED    1  8
  AMP PEAK 17(12P12.1) WILD-TYPE  2 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(12P12.1) MUTATED      1    8
  AMP PEAK 17(12P12.1) WILD-TYPE    2   11
        clus
vv       AMP PEAK 17(12P12.1) MUTATED AMP PEAK 17(12P12.1) WILD-TYPE
  FEMALE                            1                              2
  MALE                              8                             11
D16V7, continuous

Clustering(17) Variable = AMP PEAK 18(14Q22.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 18(14Q22.1) MUTATED    2  3
  AMP PEAK 18(14Q22.1) WILD-TYPE 10  3
  AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE 
                             5                             13 
  AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE 
                             3                              3 
$`AMP PEAK 18(14Q22.1) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        0.03         3.16         7.10         7.43         0.07 

$`AMP PEAK 18(14Q22.1) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.26         0.53         0.79         0.36         3.48         3.68 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        4.08        18.35         3.32         1.38        30.71        29.00 
TCGA-LN-A4A2 
        0.13 

  AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE 
                          0.03                           0.13 
  AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE 
                          7.43                          30.71 
  AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE 
                          3.16                           3.32 
[1] "0.0 - 7.4 (3.2)"  "0.1 - 30.7 (3.3)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 18(14Q22.1) MUTATED" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 18(14Q22.1) WILD-TYPE"   "AMP PEAK 18(14Q22.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK 18(14Q22.1) MUTATED"   "AMP PEAK 18(14Q22.1) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 18(14Q22.1) WILD-TYPE"   "AMP PEAK 18(14Q22.1) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 18(14Q22.1) MUTATED" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 18(14Q22.1) WILD-TYPE"   "AMP PEAK 18(14Q22.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK 18(14Q22.1) MUTATED"   "AMP PEAK 18(14Q22.1) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 18(14Q22.1) WILD-TYPE"   "AMP PEAK 18(14Q22.1) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 18(14Q22.1) MUTATED" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 18(14Q22.1) WILD-TYPE"   "AMP PEAK 18(14Q22.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 18(14Q22.1) WILD-TYPE" "AMP PEAK 18(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "AMP PEAK 18(14Q22.1) MUTATED"   "AMP PEAK 18(14Q22.1) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 18(14Q22.1) WILD-TYPE"   "AMP PEAK 18(14Q22.1) MUTATED" 
[1] "hr=" "3.7"
D17V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 18(14Q22.1) MUTATED          1        0         1         3
  AMP PEAK 18(14Q22.1) WILD-TYPE        1        1         2         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 18(14Q22.1) MUTATED            2          0          0
  AMP PEAK 18(14Q22.1) WILD-TYPE          3          3          1
D17V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 18(14Q22.1) MUTATED    1  4     2
  AMP PEAK 18(14Q22.1) WILD-TYPE  3  3     9
D17V4, multiclass
       clus
vv      AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE
  T1                               1                              3
  T2                               4                              3
  T3+T4                            2                              9
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 18(14Q22.1) MUTATED    4  3     0
  AMP PEAK 18(14Q22.1) WILD-TYPE  4  7     4
D17V5, multiclass
       clus
vv      AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE
  N0                               4                              4
  N1                               3                              7
  N2+N3                            0                              4
D17V6, binary
                                cls
clus                              0  1
  AMP PEAK 18(14Q22.1) MUTATED    1  6
  AMP PEAK 18(14Q22.1) WILD-TYPE  2 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(14Q22.1) MUTATED      1    6
  AMP PEAK 18(14Q22.1) WILD-TYPE    2   13
        clus
vv       AMP PEAK 18(14Q22.1) MUTATED AMP PEAK 18(14Q22.1) WILD-TYPE
  FEMALE                            1                              2
  MALE                              6                             13
D17V7, continuous

Clustering(18) Variable = AMP PEAK 19(17Q12) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                          0 1
  AMP PEAK 19(17Q12) MUTATED   7 3
  AMP PEAK 19(17Q12) WILD-TYPE 5 3
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          10                            8 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                           3                            3 
$`AMP PEAK 19(17Q12) MUTATED`
TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.53         0.36         3.48        18.35         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A2 
       30.71        29.00         7.10         0.13 

$`AMP PEAK 19(17Q12) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR 
        0.03         0.26         0.79         3.68         4.08         3.16 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                        0.13                         0.03 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                       30.71                         7.43 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                       3.400                        1.975 
[1] "0.1 - 30.7 (3.4)" "0.0 - 7.4 (2.0)" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 19(17Q12) WILD-TYPE" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-IG-A625                   TCGA-L5-A4OE 
  "AMP PEAK 19(17Q12) MUTATED"   "AMP PEAK 19(17Q12) MUTATED" 
                  TCGA-L5-A4OF                   TCGA-L5-A4OM 
"AMP PEAK 19(17Q12) WILD-TYPE" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
  "AMP PEAK 19(17Q12) MUTATED"   "AMP PEAK 19(17Q12) MUTATED" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OR 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-L5-A4OS                   TCGA-L5-A4OU 
  "AMP PEAK 19(17Q12) MUTATED"   "AMP PEAK 19(17Q12) MUTATED" 
                  TCGA-L5-A4OW                   TCGA-L5-A4OX 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-LN-A4A2                   TCGA-LN-A4A9 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 19(17Q12) WILD-TYPE" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-IG-A625                   TCGA-L5-A4OE 
  "AMP PEAK 19(17Q12) MUTATED"   "AMP PEAK 19(17Q12) MUTATED" 
                  TCGA-L5-A4OF                   TCGA-L5-A4OM 
"AMP PEAK 19(17Q12) WILD-TYPE" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
  "AMP PEAK 19(17Q12) MUTATED"   "AMP PEAK 19(17Q12) MUTATED" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OR 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-L5-A4OS                   TCGA-L5-A4OU 
  "AMP PEAK 19(17Q12) MUTATED"   "AMP PEAK 19(17Q12) MUTATED" 
                  TCGA-L5-A4OW                   TCGA-L5-A4OX 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-LN-A4A2                   TCGA-LN-A4A9 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 19(17Q12) WILD-TYPE" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-IG-A625                   TCGA-L5-A4OE 
  "AMP PEAK 19(17Q12) MUTATED"   "AMP PEAK 19(17Q12) MUTATED" 
                  TCGA-L5-A4OF                   TCGA-L5-A4OM 
"AMP PEAK 19(17Q12) WILD-TYPE" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
  "AMP PEAK 19(17Q12) MUTATED"   "AMP PEAK 19(17Q12) MUTATED" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OR 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-L5-A4OS                   TCGA-L5-A4OU 
  "AMP PEAK 19(17Q12) MUTATED"   "AMP PEAK 19(17Q12) MUTATED" 
                  TCGA-L5-A4OW                   TCGA-L5-A4OX 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
                  TCGA-LN-A4A2                   TCGA-LN-A4A9 
  "AMP PEAK 19(17Q12) MUTATED" "AMP PEAK 19(17Q12) WILD-TYPE" 
[1] "hr=" "3.2"
D18V2, continuous
                              vv
clus                           STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 19(17Q12) MUTATED          0        0         2         4          2
  AMP PEAK 19(17Q12) WILD-TYPE        2        1         1         3          3
                              vv
clus                           STAGE IIIB STAGE IIIC
  AMP PEAK 19(17Q12) MUTATED            2          1
  AMP PEAK 19(17Q12) WILD-TYPE          1          0
D18V3, multiclass
                              vv
clus                           T1 T2 T3+T4
  AMP PEAK 19(17Q12) MUTATED    1  4     6
  AMP PEAK 19(17Q12) WILD-TYPE  3  3     5
D18V4, multiclass
       clus
vv      AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  T1                             1                            3
  T2                             4                            3
  T3+T4                          6                            5
                              vv
clus                           N0 N1 N2+N3
  AMP PEAK 19(17Q12) MUTATED    2  6     3
  AMP PEAK 19(17Q12) WILD-TYPE  6  4     1
D18V5, multiclass
       clus
vv      AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  N0                             2                            6
  N1                             6                            4
  N2+N3                          3                            1
D18V6, binary
                              cls
clus                            0  1
  AMP PEAK 19(17Q12) MUTATED    2  9
  AMP PEAK 19(17Q12) WILD-TYPE  1 10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      2    9
  AMP PEAK 19(17Q12) WILD-TYPE    1   10
        clus
vv       AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  FEMALE                          2                            1
  MALE                            9                           10
D18V7, continuous

Clustering(19) Variable = AMP PEAK 20(17Q24.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 20(17Q24.3) MUTATED   8 3
  AMP PEAK 20(17Q24.3) WILD-TYPE 4 3
  AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE 
                            11                              7 
  AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE 
                             3                              3 
$`AMP PEAK 20(17Q24.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4ON 
        0.03         0.53         0.79         0.36         3.48        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.32         1.38        29.00         0.13         0.07 

$`AMP PEAK 20(17Q24.3) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        0.26         3.68         4.08         3.16        30.71         7.10 
TCGA-L5-A4OX 
        7.43 

  AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE 
                          0.03                           0.26 
  AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE 
                         29.00                          30.71 
  AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE 
                          0.79                           4.08 
[1] "0.0 - 29.0 (0.8)" "0.3 - 30.7 (4.1)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 20(17Q24.3) MUTATED" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 20(17Q24.3) WILD-TYPE" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "AMP PEAK 20(17Q24.3) MUTATED" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 20(17Q24.3) WILD-TYPE"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 20(17Q24.3) WILD-TYPE" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 20(17Q24.3) MUTATED" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 20(17Q24.3) WILD-TYPE" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "AMP PEAK 20(17Q24.3) MUTATED" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 20(17Q24.3) WILD-TYPE"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 20(17Q24.3) WILD-TYPE" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 20(17Q24.3) MUTATED" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 20(17Q24.3) WILD-TYPE" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "AMP PEAK 20(17Q24.3) MUTATED" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 20(17Q24.3) WILD-TYPE"   "AMP PEAK 20(17Q24.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 20(17Q24.3) WILD-TYPE" "AMP PEAK 20(17Q24.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "AMP PEAK 20(17Q24.3) MUTATED"   "AMP PEAK 20(17Q24.3) MUTATED" 
[1] "hr=" "1.1"
D19V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 20(17Q24.3) MUTATED          0        1         3         3
  AMP PEAK 20(17Q24.3) WILD-TYPE        2        0         0         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 20(17Q24.3) MUTATED            2          2          1
  AMP PEAK 20(17Q24.3) WILD-TYPE          3          1          0
D19V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 20(17Q24.3) MUTATED    1  4     7
  AMP PEAK 20(17Q24.3) WILD-TYPE  3  3     4
D19V4, multiclass
       clus
vv      AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE
  T1                               1                              3
  T2                               4                              3
  T3+T4                            7                              4
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 20(17Q24.3) MUTATED    4  5     3
  AMP PEAK 20(17Q24.3) WILD-TYPE  4  5     1
D19V5, multiclass
       clus
vv      AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE
  N0                               4                              4
  N1                               5                              5
  N2+N3                            3                              1
D19V6, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q24.3) MUTATED    0 12
  AMP PEAK 20(17Q24.3) WILD-TYPE  3  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.3) MUTATED      0   12
  AMP PEAK 20(17Q24.3) WILD-TYPE    3    7
        clus
vv       AMP PEAK 20(17Q24.3) MUTATED AMP PEAK 20(17Q24.3) WILD-TYPE
  FEMALE                            0                              3
  MALE                             12                              7
D19V7, continuous

Clustering(20) Variable = AMP PEAK 21(18P11.32) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                             0 1
  AMP PEAK 21(18P11.32) MUTATED   4 3
  AMP PEAK 21(18P11.32) WILD-TYPE 8 3
  AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE 
                              7                              11 
  AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE 
                              3                               3 
$`AMP PEAK 21(18P11.32) MUTATED`
TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.53         0.36         4.08         3.32         1.38         3.16 
TCGA-L5-A4OW 
        7.10 

$`AMP PEAK 21(18P11.32) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON 
        0.03         0.26         0.79         3.48         3.68        18.35 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       30.71        29.00         7.43         0.13         0.07 

  AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE 
                           0.36                            0.03 
  AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE 
                           7.10                           30.71 
  AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE 
                           3.16                            3.48 
[1] "0.4 - 7.1 (3.2)"  "0.0 - 30.7 (3.5)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"AMP PEAK 21(18P11.32) WILD-TYPE" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "AMP PEAK 21(18P11.32) MUTATED" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
  "AMP PEAK 21(18P11.32) MUTATED" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"AMP PEAK 21(18P11.32) WILD-TYPE"   "AMP PEAK 21(18P11.32) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"AMP PEAK 21(18P11.32) WILD-TYPE"   "AMP PEAK 21(18P11.32) MUTATED" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
  "AMP PEAK 21(18P11.32) MUTATED"   "AMP PEAK 21(18P11.32) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"AMP PEAK 21(18P11.32) WILD-TYPE" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
  "AMP PEAK 21(18P11.32) MUTATED" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
"AMP PEAK 21(18P11.32) WILD-TYPE" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"AMP PEAK 21(18P11.32) WILD-TYPE" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "AMP PEAK 21(18P11.32) MUTATED" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
  "AMP PEAK 21(18P11.32) MUTATED" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"AMP PEAK 21(18P11.32) WILD-TYPE"   "AMP PEAK 21(18P11.32) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"AMP PEAK 21(18P11.32) WILD-TYPE"   "AMP PEAK 21(18P11.32) MUTATED" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
  "AMP PEAK 21(18P11.32) MUTATED"   "AMP PEAK 21(18P11.32) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"AMP PEAK 21(18P11.32) WILD-TYPE" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
  "AMP PEAK 21(18P11.32) MUTATED" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
"AMP PEAK 21(18P11.32) WILD-TYPE" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"AMP PEAK 21(18P11.32) WILD-TYPE" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "AMP PEAK 21(18P11.32) MUTATED" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
  "AMP PEAK 21(18P11.32) MUTATED" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"AMP PEAK 21(18P11.32) WILD-TYPE"   "AMP PEAK 21(18P11.32) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"AMP PEAK 21(18P11.32) WILD-TYPE"   "AMP PEAK 21(18P11.32) MUTATED" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
  "AMP PEAK 21(18P11.32) MUTATED"   "AMP PEAK 21(18P11.32) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"AMP PEAK 21(18P11.32) WILD-TYPE" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
  "AMP PEAK 21(18P11.32) MUTATED" "AMP PEAK 21(18P11.32) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
"AMP PEAK 21(18P11.32) WILD-TYPE" "AMP PEAK 21(18P11.32) WILD-TYPE" 
[1] "hr=" "5.6"
D20V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 21(18P11.32) MUTATED          2        0         0         1
  AMP PEAK 21(18P11.32) WILD-TYPE        0        1         3         6
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 21(18P11.32) MUTATED            2          1          1
  AMP PEAK 21(18P11.32) WILD-TYPE          3          2          0
D20V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  AMP PEAK 21(18P11.32) MUTATED    2  2     3
  AMP PEAK 21(18P11.32) WILD-TYPE  2  5     8
D20V4, multiclass
       clus
vv      AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE
  T1                                2                               2
  T2                                2                               5
  T3+T4                             3                               8
                                 vv
clus                              N0 N1 N2+N3
  AMP PEAK 21(18P11.32) MUTATED    2  3     2
  AMP PEAK 21(18P11.32) WILD-TYPE  6  7     2
D20V5, multiclass
       clus
vv      AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE
  N0                                2                               6
  N1                                3                               7
  N2+N3                             2                               2
D20V6, binary
                                 cls
clus                               0  1
  AMP PEAK 21(18P11.32) MUTATED    2  5
  AMP PEAK 21(18P11.32) WILD-TYPE  1 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(18P11.32) MUTATED      2    5
  AMP PEAK 21(18P11.32) WILD-TYPE    1   14
        clus
vv       AMP PEAK 21(18P11.32) MUTATED AMP PEAK 21(18P11.32) WILD-TYPE
  FEMALE                             2                               1
  MALE                               5                              14
D20V7, continuous

Clustering(21) Variable = AMP PEAK 22(18Q11.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 22(18Q11.2) MUTATED   5 2
  AMP PEAK 22(18Q11.2) WILD-TYPE 7 4
  AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE 
                             7                             11 
  AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE 
                             2                              4 
$`AMP PEAK 22(18Q11.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.36         3.48         4.08        18.35         3.32 
TCGA-L5-A4OR 
        3.16 

$`AMP PEAK 22(18Q11.2) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OF TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.26         0.53         0.79         3.68         1.38        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       29.00         7.10         7.43         0.13         0.07 

  AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE 
                         18.35                          30.71 
  AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE 
                          3.32                           1.38 
[1] "0.0 - 18.4 (3.3)" "0.1 - 30.7 (1.4)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 22(18Q11.2) MUTATED" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 22(18Q11.2) MUTATED"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 22(18Q11.2) WILD-TYPE"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 22(18Q11.2) MUTATED"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 22(18Q11.2) WILD-TYPE"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 22(18Q11.2) MUTATED" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 22(18Q11.2) MUTATED"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 22(18Q11.2) WILD-TYPE"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 22(18Q11.2) MUTATED"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 22(18Q11.2) WILD-TYPE"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 22(18Q11.2) MUTATED" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "AMP PEAK 22(18Q11.2) MUTATED"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 22(18Q11.2) WILD-TYPE"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "AMP PEAK 22(18Q11.2) MUTATED"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 22(18Q11.2) WILD-TYPE"   "AMP PEAK 22(18Q11.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 22(18Q11.2) WILD-TYPE" "AMP PEAK 22(18Q11.2) WILD-TYPE" 
[1] "hr=" "1.1"
D21V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 22(18Q11.2) MUTATED          2        0         0         2
  AMP PEAK 22(18Q11.2) WILD-TYPE        0        1         3         5
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 22(18Q11.2) MUTATED            0          2          1
  AMP PEAK 22(18Q11.2) WILD-TYPE          5          1          0
D21V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 22(18Q11.2) MUTATED    3  1     3
  AMP PEAK 22(18Q11.2) WILD-TYPE  1  6     8
D21V4, multiclass
       clus
vv      AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE
  T1                               3                              1
  T2                               1                              6
  T3+T4                            3                              8
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 22(18Q11.2) MUTATED    2  2     3
  AMP PEAK 22(18Q11.2) WILD-TYPE  6  8     1
D21V5, multiclass
       clus
vv      AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE
  N0                               2                              6
  N1                               2                              8
  N2+N3                            3                              1
D21V6, binary
                                cls
clus                              0  1
  AMP PEAK 22(18Q11.2) MUTATED    1  6
  AMP PEAK 22(18Q11.2) WILD-TYPE  2 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(18Q11.2) MUTATED      1    6
  AMP PEAK 22(18Q11.2) WILD-TYPE    2   13
        clus
vv       AMP PEAK 22(18Q11.2) MUTATED AMP PEAK 22(18Q11.2) WILD-TYPE
  FEMALE                            1                              2
  MALE                              6                             13
D21V7, continuous

Clustering(22) Variable = AMP PEAK 23(19P13.2) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 23(19P13.2) MUTATED    1  1
  AMP PEAK 23(19P13.2) WILD-TYPE 11  5
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                             2                             16 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                             1                              5 
$`AMP PEAK 23(19P13.2) MUTATED`
TCGA-L5-A4OR TCGA-L5-A4OU 
        3.16        29.00 

$`AMP PEAK 23(19P13.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE 
        0.03         0.26         0.53         0.79         0.36         3.48 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
        3.68         4.08        18.35         3.32         1.38        30.71 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.10         7.43         0.13         0.07 

  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                          3.16                           0.03 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                         29.00                          30.71 
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                         16.08                           2.35 
[1] "3.2 - 29.0 (16.1)" "0.0 - 30.7 (2.3)" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 23(19P13.2) WILD-TYPE"   "AMP PEAK 23(19P13.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 23(19P13.2) WILD-TYPE"   "AMP PEAK 23(19P13.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 23(19P13.2) WILD-TYPE"   "AMP PEAK 23(19P13.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 23(19P13.2) WILD-TYPE"   "AMP PEAK 23(19P13.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"AMP PEAK 23(19P13.2) WILD-TYPE"   "AMP PEAK 23(19P13.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"AMP PEAK 23(19P13.2) WILD-TYPE"   "AMP PEAK 23(19P13.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
[1] "Remove cluster labels:"       "AMP PEAK 23(19P13.2) MUTATED"
clus
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                             2                             16 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OS 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
D22V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 23(19P13.2) MUTATED          1        0         1         1
  AMP PEAK 23(19P13.2) WILD-TYPE        1        1         2         6
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 23(19P13.2) MUTATED            0          0          0
  AMP PEAK 23(19P13.2) WILD-TYPE          5          3          1
D22V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 23(19P13.2) MUTATED    1  1     1
  AMP PEAK 23(19P13.2) WILD-TYPE  3  6    10
D22V4, multiclass
       clus
vv      AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE
  T1                               1                              3
  T2                               1                              6
  T3+T4                            1                             10
                                vv
clus                             N0 N1 N2+N3
  AMP PEAK 23(19P13.2) MUTATED    2  1     0
  AMP PEAK 23(19P13.2) WILD-TYPE  6  9     4
D22V5, multiclass
       clus
vv      AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE
  N0                               2                              6
  N1                               1                              9
  N2+N3                            0                              4
D22V6, binary
                                cls
clus                              0  1
  AMP PEAK 23(19P13.2) MUTATED    0  3
  AMP PEAK 23(19P13.2) WILD-TYPE  3 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(19P13.2) MUTATED      0    3
  AMP PEAK 23(19P13.2) WILD-TYPE    3   16
        clus
vv       AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE
  FEMALE                            0                              3
  MALE                              3                             16
D22V7, continuous
[1] "Remove cluster labels:"       "AMP PEAK 23(19P13.2) MUTATED"
clus
  AMP PEAK 23(19P13.2) MUTATED AMP PEAK 23(19P13.2) WILD-TYPE 
                             1                             13 
                    TCGA-IG-A3Y9                     TCGA-IG-A3YA 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A50L 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-IG-A5B8                     TCGA-L5-A4OE 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"AMP PEAK 23(19P13.2) WILD-TYPE" "AMP PEAK 23(19P13.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 23(19P13.2) WILD-TYPE" 

Clustering(23) Variable = AMP PEAK 24(19Q12) MUTATION ANALYSIS
D23V1, survival
                              sevent
clus2                          0 1
  AMP PEAK 24(19Q12) MUTATED   5 3
  AMP PEAK 24(19Q12) WILD-TYPE 7 3
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                           8                           10 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                           3                            3 
$`AMP PEAK 24(19Q12) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.48         3.68        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS 
        3.16        30.71 

$`AMP PEAK 24(19Q12) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OM TCGA-L5-A4OU 
        0.03         0.53         0.79         0.36         4.08        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.10         7.43         0.13         0.07 

  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                        0.26                         0.03 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                       30.71                        29.00 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                        3.40                         0.66 
[1] "0.3 - 30.7 (3.4)" "0.0 - 29.0 (0.7)"
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-IG-A625                   TCGA-L5-A4OE 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OF                   TCGA-L5-A4OM 
  "AMP PEAK 24(19Q12) MUTATED" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OR 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OS                   TCGA-L5-A4OU 
  "AMP PEAK 24(19Q12) MUTATED" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-L5-A4OW                   TCGA-L5-A4OX 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-LN-A4A2                   TCGA-LN-A4A9 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-IG-A625                   TCGA-L5-A4OE 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OF                   TCGA-L5-A4OM 
  "AMP PEAK 24(19Q12) MUTATED" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OR 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OS                   TCGA-L5-A4OU 
  "AMP PEAK 24(19Q12) MUTATED" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-L5-A4OW                   TCGA-L5-A4OX 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-LN-A4A2                   TCGA-LN-A4A9 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-IG-A50L                   TCGA-IG-A5B8 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-IG-A625                   TCGA-L5-A4OE 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OF                   TCGA-L5-A4OM 
  "AMP PEAK 24(19Q12) MUTATED" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-L5-A4ON                   TCGA-L5-A4OO 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OR 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OS                   TCGA-L5-A4OU 
  "AMP PEAK 24(19Q12) MUTATED" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-L5-A4OW                   TCGA-L5-A4OX 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-LN-A4A2                   TCGA-LN-A4A9 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
[1] "hr=" "1.3"
D23V2, continuous
                              vv
clus                           STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 24(19Q12) MUTATED          1        0         0         3          1
  AMP PEAK 24(19Q12) WILD-TYPE        1        1         3         4          4
                              vv
clus                           STAGE IIIB STAGE IIIC
  AMP PEAK 24(19Q12) MUTATED            2          1
  AMP PEAK 24(19Q12) WILD-TYPE          1          0
D23V3, multiclass
                              vv
clus                           T1 T2 T3+T4
  AMP PEAK 24(19Q12) MUTATED    3  2     3
  AMP PEAK 24(19Q12) WILD-TYPE  1  5     8
D23V4, multiclass
       clus
vv      AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  T1                             3                            1
  T2                             2                            5
  T3+T4                          3                            8
                              vv
clus                           N0 N1 N2+N3
  AMP PEAK 24(19Q12) MUTATED    1  4     3
  AMP PEAK 24(19Q12) WILD-TYPE  7  6     1
D23V5, multiclass
       clus
vv      AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  N0                             1                            7
  N1                             4                            6
  N2+N3                          3                            1
D23V6, binary
                              cls
clus                            0  1
  AMP PEAK 24(19Q12) MUTATED    1  7
  AMP PEAK 24(19Q12) WILD-TYPE  2 12
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(19Q12) MUTATED      1    7
  AMP PEAK 24(19Q12) WILD-TYPE    2   12
        clus
vv       AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  FEMALE                          1                            2
  MALE                            7                           12
D23V7, continuous

Clustering(24) Variable = AMP PEAK 25(XP11.4) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 25(XP11.4) MUTATED    1  3
  AMP PEAK 25(XP11.4) WILD-TYPE 11  3
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                            4                            14 
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                            3                             3 
$`AMP PEAK 25(XP11.4) MUTATED`
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW TCGA-LN-A4A9 
        1.38         3.16         7.10         0.07 

$`AMP PEAK 25(XP11.4) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE 
        0.03         0.26         0.53         0.79         0.36         3.48 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OS TCGA-L5-A4OU 
        3.68         4.08        18.35         3.32        30.71        29.00 
TCGA-L5-A4OX TCGA-LN-A4A2 
        7.43         0.13 

  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                         7.10                         30.71 
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                         2.27                          3.40 
[1] "0.1 - 7.1 (2.3)"  "0.0 - 30.7 (3.4)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK 25(XP11.4) MUTATED"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK 25(XP11.4) MUTATED" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"AMP PEAK 25(XP11.4) WILD-TYPE"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK 25(XP11.4) MUTATED"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK 25(XP11.4) MUTATED" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"AMP PEAK 25(XP11.4) WILD-TYPE"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "AMP PEAK 25(XP11.4) MUTATED"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "AMP PEAK 25(XP11.4) MUTATED" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"AMP PEAK 25(XP11.4) WILD-TYPE"   "AMP PEAK 25(XP11.4) MUTATED" 
[1] "hr=" "10" 
D24V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 25(XP11.4) MUTATED          1        0         1         1
  AMP PEAK 25(XP11.4) WILD-TYPE        1        1         2         6
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 25(XP11.4) MUTATED            1          0          0
  AMP PEAK 25(XP11.4) WILD-TYPE          4          3          1
D24V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK 25(XP11.4) MUTATED    1  3     0
  AMP PEAK 25(XP11.4) WILD-TYPE  3  4    11
D24V4, multiclass
       clus
vv      AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE
  T1                              1                             3
  T2                              3                             4
  T3+T4                           0                            11
                               vv
clus                            N0 N1 N2+N3
  AMP PEAK 25(XP11.4) MUTATED    2  2     0
  AMP PEAK 25(XP11.4) WILD-TYPE  6  8     4
D24V5, multiclass
       clus
vv      AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE
  N0                              2                             6
  N1                              2                             8
  N2+N3                           0                             4
D24V6, binary
                               cls
clus                             0  1
  AMP PEAK 25(XP11.4) MUTATED    1  3
  AMP PEAK 25(XP11.4) WILD-TYPE  2 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XP11.4) MUTATED      1    3
  AMP PEAK 25(XP11.4) WILD-TYPE    2   16
        clus
vv       AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE
  FEMALE                           1                             2
  MALE                             3                            16
D24V7, continuous

Clustering(25) Variable = DEL PEAK  1(1P36.13) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                            0 1
  DEL PEAK  1(1P36.13) MUTATED   7 3
  DEL PEAK  1(1P36.13) WILD-TYPE 5 3
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            10                              8 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                             3                              3 
$`DEL PEAK  1(1P36.13) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.26         0.53         0.36         3.48         3.68 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        29.00         7.10         7.43 

$`DEL PEAK  1(1P36.13) WILD-TYPE`
TCGA-IG-A5B8 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.79         4.08        18.35         3.32         1.38        30.71 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                          3.32                           2.35 
[1] "0.0 - 29.0 (3.3)" "0.1 - 30.7 (2.3)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK  1(1P36.13) WILD-TYPE"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK  1(1P36.13) WILD-TYPE"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK  1(1P36.13) WILD-TYPE"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK  1(1P36.13) WILD-TYPE"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK  1(1P36.13) WILD-TYPE"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK  1(1P36.13) WILD-TYPE"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
[1] "hr=" "1.1"
D25V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  1(1P36.13) MUTATED          1        0         1         4
  DEL PEAK  1(1P36.13) WILD-TYPE        1        1         2         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  1(1P36.13) MUTATED            1          3          0
  DEL PEAK  1(1P36.13) WILD-TYPE          4          0          1
D25V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK  1(1P36.13) MUTATED    2  3     5
  DEL PEAK  1(1P36.13) WILD-TYPE  2  4     6
D25V4, multiclass
       clus
vv      DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  T1                               2                              2
  T2                               3                              4
  T3+T4                            5                              6
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK  1(1P36.13) MUTATED    2  5     3
  DEL PEAK  1(1P36.13) WILD-TYPE  6  5     1
D25V5, multiclass
       clus
vv      DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  N0                               2                              6
  N1                               5                              5
  N2+N3                            3                              1
D25V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.13) MUTATED    1  9
  DEL PEAK  1(1P36.13) WILD-TYPE  2 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED      1    9
  DEL PEAK  1(1P36.13) WILD-TYPE    2   10
        clus
vv       DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  FEMALE                            1                              2
  MALE                              9                             10
D25V7, continuous

Clustering(26) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  2(1P13.2) MUTATED   6 3
  DEL PEAK  2(1P13.2) WILD-TYPE 6 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            9                             9 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            3                             3 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OU 
        0.03         0.26         0.53         0.79         3.48        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        7.10         7.43         0.07 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.36         3.68         4.08        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-LN-A4A2 
        3.16        30.71         0.13 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.03                          0.13 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        29.00                         30.71 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.79                          3.32 
[1] "0.0 - 29.0 (0.8)" "0.1 - 30.7 (3.3)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
[1] "hr=" "1.3"
D26V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  2(1P13.2) MUTATED          0        1         2         3
  DEL PEAK  2(1P13.2) WILD-TYPE        2        0         1         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  2(1P13.2) MUTATED            2          2          0
  DEL PEAK  2(1P13.2) WILD-TYPE          3          1          1
D26V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  2(1P13.2) MUTATED    0  4     6
  DEL PEAK  2(1P13.2) WILD-TYPE  4  3     5
D26V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                              0                             4
  T2                              4                             3
  T3+T4                           6                             5
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  2(1P13.2) MUTATED    3  5     2
  DEL PEAK  2(1P13.2) WILD-TYPE  5  5     2
D26V5, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                              3                             5
  N1                              5                             5
  N2+N3                           2                             2
D26V6, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    1  9
  DEL PEAK  2(1P13.2) WILD-TYPE  2 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      1    9
  DEL PEAK  2(1P13.2) WILD-TYPE    2   10
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                           1                             2
  MALE                             9                            10
D26V7, continuous

Clustering(27) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                         0 1
  DEL PEAK  3(1Q44) MUTATED   3 0
  DEL PEAK  3(1Q44) WILD-TYPE 9 6
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          3                          15 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          0                           6 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OO 
        0.26         3.48         3.32 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OM 
        0.03         0.53         0.79         0.36         3.68         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         1.38         3.16        30.71        29.00         7.10 
TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.43         0.13         0.07 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       0.26                        0.03 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       3.48                       30.71 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       3.32                        3.16 
[1] "0.3 - 3.5 (3.3)"  "0.0 - 30.7 (3.2)"
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-IG-A50L                  TCGA-IG-A5B8 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A625                  TCGA-L5-A4OE 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-L5-A4OF                  TCGA-L5-A4OM 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4ON                  TCGA-L5-A4OO 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-L5-A4OQ                  TCGA-L5-A4OR 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OS                  TCGA-L5-A4OU 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OW                  TCGA-L5-A4OX 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-LN-A4A2                  TCGA-LN-A4A9 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-IG-A50L                  TCGA-IG-A5B8 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A625                  TCGA-L5-A4OE 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-L5-A4OF                  TCGA-L5-A4OM 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4ON                  TCGA-L5-A4OO 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-L5-A4OQ                  TCGA-L5-A4OR 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OS                  TCGA-L5-A4OU 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OW                  TCGA-L5-A4OX 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-LN-A4A2                  TCGA-LN-A4A9 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-IG-A50L                  TCGA-IG-A5B8 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A625                  TCGA-L5-A4OE 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-L5-A4OF                  TCGA-L5-A4OM 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4ON                  TCGA-L5-A4OO 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-L5-A4OQ                  TCGA-L5-A4OR 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OS                  TCGA-L5-A4OU 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OW                  TCGA-L5-A4OX 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-LN-A4A2                  TCGA-LN-A4A9 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
[1] "hr="     "2.5e+08"
D27V2, continuous
                             vv
clus                          STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK  3(1Q44) MUTATED          0        0         0         0          0
  DEL PEAK  3(1Q44) WILD-TYPE        2        1         3         7          5
                             vv
clus                          STAGE IIIB STAGE IIIC
  DEL PEAK  3(1Q44) MUTATED            2          1
  DEL PEAK  3(1Q44) WILD-TYPE          1          0
D27V3, multiclass
                             vv
clus                          T1 T2 T3+T4
  DEL PEAK  3(1Q44) MUTATED    0  0     3
  DEL PEAK  3(1Q44) WILD-TYPE  4  7     8
D27V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T1                            0                           4
  T2                            0                           7
  T3+T4                         3                           8
                             vv
clus                          N0 N1 N2+N3
  DEL PEAK  3(1Q44) MUTATED    0  0     3
  DEL PEAK  3(1Q44) WILD-TYPE  8 10     1
D27V5, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                            0                           8
  N1                            0                          10
  N2+N3                         3                           1
D27V6, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q44) MUTATED    0  3
  DEL PEAK  3(1Q44) WILD-TYPE  3 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0    3
  DEL PEAK  3(1Q44) WILD-TYPE    3   16
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                         0                           3
  MALE                           3                          16
D27V7, continuous
[1] "Remove cluster labels:"    "DEL PEAK  3(1Q44) MUTATED"
clus
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          2                          12 
                 TCGA-IG-A3Y9                  TCGA-IG-A3YA 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A4P3                  TCGA-IG-A50L 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A5B8                  TCGA-L5-A4OM 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4ON                  TCGA-L5-A4OQ 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OU                  TCGA-L5-A4OW 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OX                  TCGA-LN-A4A9 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 

Clustering(28) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  4(2Q22.1) MUTATED   4 2
  DEL PEAK  4(2Q22.1) WILD-TYPE 8 4
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            6                            12 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            2                             4 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OS TCGA-L5-A4OX 
        0.03         0.53         0.79         3.48        30.71         7.43 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         0.36         3.68         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A2 TCGA-LN-A4A9 
        1.38         3.16        29.00         7.10         0.13         0.07 

  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 
                        30.71                         29.00 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        2.135                         3.240 
[1] "0.0 - 30.7 (2.1)" "0.1 - 29.0 (3.2)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  4(2Q22.1) MUTATED"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  4(2Q22.1) WILD-TYPE"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK  4(2Q22.1) WILD-TYPE"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  4(2Q22.1) MUTATED"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  4(2Q22.1) WILD-TYPE"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK  4(2Q22.1) WILD-TYPE"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  4(2Q22.1) MUTATED"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  4(2Q22.1) WILD-TYPE"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK  4(2Q22.1) WILD-TYPE"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
[1] "hr=" "1.1"
D28V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  4(2Q22.1) MUTATED          0        1         0         4
  DEL PEAK  4(2Q22.1) WILD-TYPE        2        0         3         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  4(2Q22.1) MUTATED            3          1          0
  DEL PEAK  4(2Q22.1) WILD-TYPE          2          2          1
D28V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  4(2Q22.1) MUTATED    0  4     5
  DEL PEAK  4(2Q22.1) WILD-TYPE  4  3     6
D28V4, multiclass
       clus
vv      DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T1                              0                             4
  T2                              4                             3
  T3+T4                           5                             6
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  4(2Q22.1) MUTATED    2  6     1
  DEL PEAK  4(2Q22.1) WILD-TYPE  6  4     3
D28V5, multiclass
       clus
vv      DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                              2                             6
  N1                              6                             4
  N2+N3                           1                             3
D28V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED    1  8
  DEL PEAK  4(2Q22.1) WILD-TYPE  2 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      1    8
  DEL PEAK  4(2Q22.1) WILD-TYPE    2   11
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                           1                             2
  MALE                             8                            11
D28V7, continuous

Clustering(29) Variable = DEL PEAK  5(2Q33.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q33.3) MUTATED    2  1
  DEL PEAK  5(2Q33.3) WILD-TYPE 10  5
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                            3                            15 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                            1                             5 
$`DEL PEAK  5(2Q33.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A4OS 
        0.03         0.79        30.71 

$`DEL PEAK  5(2Q33.3) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM 
        0.26         0.53         0.36         3.48         3.68         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         3.32         1.38         3.16        29.00         7.10 
TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.43         0.13         0.07 

  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 
                        30.71                         29.00 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                         0.79                          3.32 
[1] "0.0 - 30.7 (0.8)" "0.1 - 29.0 (3.3)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  5(2Q33.3) MUTATED" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK  5(2Q33.3) WILD-TYPE"   "DEL PEAK  5(2Q33.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK  5(2Q33.3) MUTATED" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  5(2Q33.3) MUTATED" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK  5(2Q33.3) WILD-TYPE"   "DEL PEAK  5(2Q33.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK  5(2Q33.3) MUTATED" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  5(2Q33.3) MUTATED" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK  5(2Q33.3) WILD-TYPE"   "DEL PEAK  5(2Q33.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK  5(2Q33.3) MUTATED" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK  5(2Q33.3) WILD-TYPE" "DEL PEAK  5(2Q33.3) WILD-TYPE" 
[1] "hr=" "1.2"
D29V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  5(2Q33.3) MUTATED          0        1         0         2
  DEL PEAK  5(2Q33.3) WILD-TYPE        2        0         3         5
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  5(2Q33.3) MUTATED            2          0          0
  DEL PEAK  5(2Q33.3) WILD-TYPE          3          3          1
D29V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  5(2Q33.3) MUTATED    0  2     3
  DEL PEAK  5(2Q33.3) WILD-TYPE  4  5     8
D29V4, multiclass
       clus
vv      DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  T1                              0                             4
  T2                              2                             5
  T3+T4                           3                             8
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  5(2Q33.3) MUTATED    2  3     0
  DEL PEAK  5(2Q33.3) WILD-TYPE  6  7     4
D29V5, multiclass
       clus
vv      DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  N0                              2                             6
  N1                              3                             7
  N2+N3                           0                             4
D29V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q33.3) MUTATED    1  4
  DEL PEAK  5(2Q33.3) WILD-TYPE  2 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED      1    4
  DEL PEAK  5(2Q33.3) WILD-TYPE    2   15
        clus
vv       DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  FEMALE                           1                             2
  MALE                             4                            15
D29V7, continuous

Clustering(30) Variable = DEL PEAK  6(3P14.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  6(3P14.3) MUTATED   7 4
  DEL PEAK  6(3P14.3) WILD-TYPE 5 2
  DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE 
                           11                             7 
  DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE 
                            4                             2 
$`DEL PEAK  6(3P14.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OF TCGA-L5-A4OM 
        0.03         0.26         0.53         0.79         3.68         4.08 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        3.32         1.38         7.10         7.43         0.13 

$`DEL PEAK  6(3P14.3) WILD-TYPE`
TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        0.36         3.48        18.35         3.16        30.71        29.00 
TCGA-LN-A4A9 
        0.07 

  DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE 
                         7.43                         30.71 
  DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE 
                         1.38                          3.48 
[1] "0.0 - 7.4 (1.4)"  "0.1 - 30.7 (3.5)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  6(3P14.3) WILD-TYPE" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  6(3P14.3) WILD-TYPE"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK  6(3P14.3) MUTATED" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK  6(3P14.3) WILD-TYPE" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK  6(3P14.3) MUTATED" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  6(3P14.3) WILD-TYPE" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  6(3P14.3) WILD-TYPE"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK  6(3P14.3) MUTATED" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK  6(3P14.3) WILD-TYPE" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK  6(3P14.3) MUTATED" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  6(3P14.3) WILD-TYPE" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  6(3P14.3) WILD-TYPE"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK  6(3P14.3) MUTATED" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK  6(3P14.3) WILD-TYPE" "DEL PEAK  6(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK  6(3P14.3) MUTATED"   "DEL PEAK  6(3P14.3) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK  6(3P14.3) MUTATED" "DEL PEAK  6(3P14.3) WILD-TYPE" 
[1] "hr=" "5.3"
D30V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  6(3P14.3) MUTATED          1        1         1         5
  DEL PEAK  6(3P14.3) WILD-TYPE        1        0         2         2
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  6(3P14.3) MUTATED            5          1          1
  DEL PEAK  6(3P14.3) WILD-TYPE          0          2          0
D30V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  6(3P14.3) MUTATED    2  5     8
  DEL PEAK  6(3P14.3) WILD-TYPE  2  2     3
D30V4, multiclass
       clus
vv      DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE
  T1                              2                             2
  T2                              5                             2
  T3+T4                           8                             3
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  6(3P14.3) MUTATED    5  8     2
  DEL PEAK  6(3P14.3) WILD-TYPE  3  2     2
D30V5, multiclass
       clus
vv      DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE
  N0                              5                             3
  N1                              8                             2
  N2+N3                           2                             2
D30V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.3) MUTATED    2 13
  DEL PEAK  6(3P14.3) WILD-TYPE  1  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.3) MUTATED      2   13
  DEL PEAK  6(3P14.3) WILD-TYPE    1    6
        clus
vv       DEL PEAK  6(3P14.3) MUTATED DEL PEAK  6(3P14.3) WILD-TYPE
  FEMALE                           2                             1
  MALE                            13                             6
D30V7, continuous

Clustering(31) Variable = DEL PEAK  7(3P14.2) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  7(3P14.2) MUTATED   8 4
  DEL PEAK  7(3P14.2) WILD-TYPE 4 2
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           12                             6 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                            4                             2 
$`DEL PEAK  7(3P14.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.26         0.53         0.79         3.48         3.68 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        4.08         3.32         1.38         7.10         7.43         0.13 

$`DEL PEAK  7(3P14.2) WILD-TYPE`
TCGA-IG-A625 TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-LN-A4A9 
        0.36        18.35         3.16        30.71        29.00         0.07 

  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                         7.43                         30.71 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                        2.350                        10.755 
[1] "0.0 - 7.4 (2.3)"   "0.1 - 30.7 (10.8)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  7(3P14.2) WILD-TYPE"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  7(3P14.2) WILD-TYPE"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK  7(3P14.2) MUTATED" "DEL PEAK  7(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK  7(3P14.2) WILD-TYPE" "DEL PEAK  7(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK  7(3P14.2) MUTATED" "DEL PEAK  7(3P14.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  7(3P14.2) WILD-TYPE"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  7(3P14.2) WILD-TYPE"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK  7(3P14.2) MUTATED" "DEL PEAK  7(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK  7(3P14.2) WILD-TYPE" "DEL PEAK  7(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK  7(3P14.2) MUTATED" "DEL PEAK  7(3P14.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK  7(3P14.2) WILD-TYPE"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK  7(3P14.2) WILD-TYPE"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK  7(3P14.2) MUTATED" "DEL PEAK  7(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK  7(3P14.2) WILD-TYPE" "DEL PEAK  7(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK  7(3P14.2) MUTATED"   "DEL PEAK  7(3P14.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK  7(3P14.2) MUTATED" "DEL PEAK  7(3P14.2) WILD-TYPE" 
[1] "hr=" "4.4"
D31V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  7(3P14.2) MUTATED          1        1         1         5
  DEL PEAK  7(3P14.2) WILD-TYPE        1        0         2         2
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  7(3P14.2) MUTATED            5          2          1
  DEL PEAK  7(3P14.2) WILD-TYPE          0          1          0
D31V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  7(3P14.2) MUTATED    2  5     9
  DEL PEAK  7(3P14.2) WILD-TYPE  2  2     2
D31V4, multiclass
       clus
vv      DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  T1                              2                             2
  T2                              5                             2
  T3+T4                           9                             2
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  7(3P14.2) MUTATED    5  8     3
  DEL PEAK  7(3P14.2) WILD-TYPE  3  2     1
D31V5, multiclass
       clus
vv      DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  N0                              5                             3
  N1                              8                             2
  N2+N3                           3                             1
D31V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.2) MUTATED    2 14
  DEL PEAK  7(3P14.2) WILD-TYPE  1  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED      2   14
  DEL PEAK  7(3P14.2) WILD-TYPE    1    5
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  FEMALE                           2                             1
  MALE                            14                             5
D31V7, continuous

Clustering(32) Variable = DEL PEAK  9(3Q26.31) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  9(3Q26.31) MUTATED    0  3
  DEL PEAK  9(3Q26.31) WILD-TYPE 12  3
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                             3                             15 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                             3                              3 
$`DEL PEAK  9(3Q26.31) MUTATED`
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OX 
       18.35         1.38         7.43 

$`DEL PEAK  9(3Q26.31) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE 
        0.03         0.26         0.53         0.79         0.36         3.48 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        3.68         4.08         3.32         3.16        30.71        29.00 
TCGA-L5-A4OW TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.10         0.13         0.07 

  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                          1.38                           0.03 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                         18.35                          30.71 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                          7.43                           3.16 
[1] "1.4 - 18.4 (7.4)" "0.0 - 30.7 (3.2)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK  9(3Q26.31) MUTATED" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "DEL PEAK  9(3Q26.31) MUTATED" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK  9(3Q26.31) WILD-TYPE"   "DEL PEAK  9(3Q26.31) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK  9(3Q26.31) MUTATED" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "DEL PEAK  9(3Q26.31) MUTATED" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK  9(3Q26.31) WILD-TYPE"   "DEL PEAK  9(3Q26.31) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK  9(3Q26.31) MUTATED" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "DEL PEAK  9(3Q26.31) MUTATED" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK  9(3Q26.31) WILD-TYPE"   "DEL PEAK  9(3Q26.31) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK  9(3Q26.31) WILD-TYPE" "DEL PEAK  9(3Q26.31) WILD-TYPE" 
[1] "hr=" "2.1"
D32V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  9(3Q26.31) MUTATED          0        0         0         2
  DEL PEAK  9(3Q26.31) WILD-TYPE        2        1         3         5
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  9(3Q26.31) MUTATED            1          0          0
  DEL PEAK  9(3Q26.31) WILD-TYPE          4          3          1
D32V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK  9(3Q26.31) MUTATED    1  2     0
  DEL PEAK  9(3Q26.31) WILD-TYPE  3  5    11
D32V4, multiclass
       clus
vv      DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  T1                               1                              3
  T2                               2                              5
  T3+T4                            0                             11
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK  9(3Q26.31) MUTATED    0  3     0
  DEL PEAK  9(3Q26.31) WILD-TYPE  8  7     4
D32V5, multiclass
       clus
vv      DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  N0                               0                              8
  N1                               3                              7
  N2+N3                            0                              4
D32V6, binary
                                cls
clus                              0  1
  DEL PEAK  9(3Q26.31) MUTATED    0  3
  DEL PEAK  9(3Q26.31) WILD-TYPE  3 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED      0    3
  DEL PEAK  9(3Q26.31) WILD-TYPE    3   16
        clus
vv       DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  FEMALE                            0                              3
  MALE                              3                             16
D32V7, continuous

Clustering(33) Variable = DEL PEAK 10(4P15.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 10(4P15.2) MUTATED   8 4
  DEL PEAK 10(4P15.2) WILD-TYPE 4 2
  DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE 
                           12                             6 
  DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE 
                            4                             2 
$`DEL PEAK 10(4P15.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE 
        0.03         0.26         0.53         0.79         0.36         3.48 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        4.08         3.32         3.16         7.10         7.43         0.13 

$`DEL PEAK 10(4P15.2) WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-LN-A4A9 
        3.68        18.35         1.38        30.71        29.00         0.07 

  DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE 
                         7.43                         30.71 
  DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE 
                        1.975                        11.015 
[1] "0.0 - 7.4 (2.0)"   "0.1 - 30.7 (11.0)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK 10(4P15.2) WILD-TYPE"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 10(4P15.2) WILD-TYPE"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 10(4P15.2) WILD-TYPE"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 10(4P15.2) WILD-TYPE" "DEL PEAK 10(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 10(4P15.2) MUTATED" "DEL PEAK 10(4P15.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK 10(4P15.2) WILD-TYPE"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 10(4P15.2) WILD-TYPE"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 10(4P15.2) WILD-TYPE"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 10(4P15.2) WILD-TYPE" "DEL PEAK 10(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 10(4P15.2) MUTATED" "DEL PEAK 10(4P15.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK 10(4P15.2) WILD-TYPE"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 10(4P15.2) WILD-TYPE"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 10(4P15.2) WILD-TYPE"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 10(4P15.2) WILD-TYPE" "DEL PEAK 10(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 10(4P15.2) MUTATED"   "DEL PEAK 10(4P15.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 10(4P15.2) MUTATED" "DEL PEAK 10(4P15.2) WILD-TYPE" 
[1] "hr=" "4.9"
D33V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 10(4P15.2) MUTATED          2        1         1         3
  DEL PEAK 10(4P15.2) WILD-TYPE        0        0         2         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 10(4P15.2) MUTATED            3          3          1
  DEL PEAK 10(4P15.2) WILD-TYPE          2          0          0
D33V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 10(4P15.2) MUTATED    2  3     9
  DEL PEAK 10(4P15.2) WILD-TYPE  2  4     2
D33V4, multiclass
       clus
vv      DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE
  T1                              2                             2
  T2                              3                             4
  T3+T4                           9                             2
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 10(4P15.2) MUTATED    6  4     4
  DEL PEAK 10(4P15.2) WILD-TYPE  2  6     0
D33V5, multiclass
       clus
vv      DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE
  N0                              6                             2
  N1                              4                             6
  N2+N3                           4                             0
D33V6, binary
                               cls
clus                             0  1
  DEL PEAK 10(4P15.2) MUTATED    2 12
  DEL PEAK 10(4P15.2) WILD-TYPE  1  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P15.2) MUTATED      2   12
  DEL PEAK 10(4P15.2) WILD-TYPE    1    7
        clus
vv       DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE
  FEMALE                           2                             1
  MALE                            12                             7
D33V7, continuous

Clustering(34) Variable = DEL PEAK 11(4Q21.23) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 11(4Q21.23) MUTATED   5 4
  DEL PEAK 11(4Q21.23) WILD-TYPE 7 2
  DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE 
                             9                              9 
  DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE 
                             4                              2 
$`DEL PEAK 11(4Q21.23) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OR 
        0.26         0.53         0.79         0.36         3.48         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
       30.71         7.10         7.43 

$`DEL PEAK 11(4Q21.23) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         3.68         4.08        18.35         3.32         1.38 
TCGA-L5-A4OU TCGA-LN-A4A2 TCGA-LN-A4A9 
       29.00         0.13         0.07 

  DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE 
                         30.71                          29.00 
  DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE 
                          3.16                           3.32 
[1] "0.3 - 30.7 (3.2)" "0.0 - 29.0 (3.3)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 11(4Q21.23) WILD-TYPE"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 11(4Q21.23) MUTATED"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "DEL PEAK 11(4Q21.23) MUTATED"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 11(4Q21.23) WILD-TYPE" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 11(4Q21.23) WILD-TYPE" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 11(4Q21.23) WILD-TYPE"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 11(4Q21.23) MUTATED" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 11(4Q21.23) MUTATED"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 11(4Q21.23) WILD-TYPE" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 11(4Q21.23) WILD-TYPE"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 11(4Q21.23) MUTATED"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "DEL PEAK 11(4Q21.23) MUTATED"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 11(4Q21.23) WILD-TYPE" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 11(4Q21.23) WILD-TYPE" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 11(4Q21.23) WILD-TYPE"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 11(4Q21.23) MUTATED" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 11(4Q21.23) MUTATED"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 11(4Q21.23) WILD-TYPE" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 11(4Q21.23) WILD-TYPE"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 11(4Q21.23) MUTATED"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "DEL PEAK 11(4Q21.23) MUTATED"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 11(4Q21.23) WILD-TYPE" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 11(4Q21.23) WILD-TYPE" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 11(4Q21.23) WILD-TYPE"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 11(4Q21.23) MUTATED" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 11(4Q21.23) MUTATED"   "DEL PEAK 11(4Q21.23) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 11(4Q21.23) WILD-TYPE" "DEL PEAK 11(4Q21.23) WILD-TYPE" 
[1] "hr=" "2.2"
D34V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 11(4Q21.23) MUTATED          1        1         0         3
  DEL PEAK 11(4Q21.23) WILD-TYPE        1        0         3         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 11(4Q21.23) MUTATED            2          3          0
  DEL PEAK 11(4Q21.23) WILD-TYPE          3          0          1
D34V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 11(4Q21.23) MUTATED    1  3     6
  DEL PEAK 11(4Q21.23) WILD-TYPE  3  4     5
D34V4, multiclass
       clus
vv      DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE
  T1                               1                              3
  T2                               3                              4
  T3+T4                            6                              5
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 11(4Q21.23) MUTATED    3  4     3
  DEL PEAK 11(4Q21.23) WILD-TYPE  5  6     1
D34V5, multiclass
       clus
vv      DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE
  N0                               3                              5
  N1                               4                              6
  N2+N3                            3                              1
D34V6, binary
                                cls
clus                              0  1
  DEL PEAK 11(4Q21.23) MUTATED    2  8
  DEL PEAK 11(4Q21.23) WILD-TYPE  1 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(4Q21.23) MUTATED      2    8
  DEL PEAK 11(4Q21.23) WILD-TYPE    1   11
        clus
vv       DEL PEAK 11(4Q21.23) MUTATED DEL PEAK 11(4Q21.23) WILD-TYPE
  FEMALE                            2                              1
  MALE                              8                             11
D34V7, continuous

Clustering(35) Variable = DEL PEAK 12(4Q22.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 12(4Q22.1) MUTATED   6 5
  DEL PEAK 12(4Q22.1) WILD-TYPE 6 1
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           11                             7 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                            5                             1 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OO 
        0.26         0.53         0.79         0.36         3.48         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        30.71         7.10         7.43 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OU TCGA-LN-A4A2 
        0.03         3.68         4.08        18.35        29.00         0.13 
TCGA-LN-A4A9 
        0.07 

  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                         0.26                          0.03 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                        30.71                         29.00 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                         3.16                          3.68 
[1] "0.3 - 30.7 (3.2)" "0.0 - 29.0 (3.7)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 12(4Q22.1) WILD-TYPE"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK 12(4Q22.1) WILD-TYPE" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 12(4Q22.1) WILD-TYPE"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 12(4Q22.1) MUTATED" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK 12(4Q22.1) WILD-TYPE" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 12(4Q22.1) WILD-TYPE"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK 12(4Q22.1) WILD-TYPE" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 12(4Q22.1) WILD-TYPE"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 12(4Q22.1) MUTATED" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK 12(4Q22.1) WILD-TYPE" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 12(4Q22.1) WILD-TYPE"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK 12(4Q22.1) WILD-TYPE" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 12(4Q22.1) WILD-TYPE"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 12(4Q22.1) MUTATED" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK 12(4Q22.1) WILD-TYPE" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
[1] "hr=" "4.3"
D35V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 12(4Q22.1) MUTATED          1        1         0         3
  DEL PEAK 12(4Q22.1) WILD-TYPE        1        0         3         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 12(4Q22.1) MUTATED            3          3          1
  DEL PEAK 12(4Q22.1) WILD-TYPE          2          0          0
D35V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 12(4Q22.1) MUTATED    1  4     7
  DEL PEAK 12(4Q22.1) WILD-TYPE  3  3     4
D35V4, multiclass
       clus
vv      DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T1                              1                             3
  T2                              4                             3
  T3+T4                           7                             4
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 12(4Q22.1) MUTATED    3  5     4
  DEL PEAK 12(4Q22.1) WILD-TYPE  5  5     0
D35V5, multiclass
       clus
vv      DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                              3                             5
  N1                              5                             5
  N2+N3                           4                             0
D35V6, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED    2 10
  DEL PEAK 12(4Q22.1) WILD-TYPE  1  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      2   10
  DEL PEAK 12(4Q22.1) WILD-TYPE    1    9
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                           2                             1
  MALE                            10                             9
D35V7, continuous

Clustering(36) Variable = DEL PEAK 13(5Q11.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 13(5Q11.2) MUTATED   8 2
  DEL PEAK 13(5Q11.2) WILD-TYPE 4 4
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           10                             8 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                            2                             4 
$`DEL PEAK 13(5Q11.2) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO 
        0.26         0.53         3.48         3.68         4.08         3.32 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-LN-A4A2 
        3.16        30.71         7.10         0.13 

$`DEL PEAK 13(5Q11.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU 
        0.03         0.79         0.36        18.35         1.38        29.00 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                        30.71                         29.00 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                        3.400                         1.085 
[1] "0.1 - 30.7 (3.4)" "0.0 - 29.0 (1.1)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 13(5Q11.2) MUTATED"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 13(5Q11.2) MUTATED"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 13(5Q11.2) MUTATED"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
[1] "hr=" "2"  
D36V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 13(5Q11.2) MUTATED          2        0         1         4
  DEL PEAK 13(5Q11.2) WILD-TYPE        0        1         2         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 13(5Q11.2) MUTATED            3          2          1
  DEL PEAK 13(5Q11.2) WILD-TYPE          2          1          0
D36V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 13(5Q11.2) MUTATED    3  3     7
  DEL PEAK 13(5Q11.2) WILD-TYPE  1  4     4
D36V4, multiclass
       clus
vv      DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  T1                              3                             1
  T2                              3                             4
  T3+T4                           7                             4
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 13(5Q11.2) MUTATED    4  6     3
  DEL PEAK 13(5Q11.2) WILD-TYPE  4  4     1
D36V5, multiclass
       clus
vv      DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  N0                              4                             4
  N1                              6                             4
  N2+N3                           3                             1
D36V6, binary
                               cls
clus                             0  1
  DEL PEAK 13(5Q11.2) MUTATED    3 10
  DEL PEAK 13(5Q11.2) WILD-TYPE  0  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED      3   10
  DEL PEAK 13(5Q11.2) WILD-TYPE    0    9
        clus
vv       DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  FEMALE                           3                             0
  MALE                            10                             9
D36V7, continuous

Clustering(37) Variable = DEL PEAK 14(5Q12.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 14(5Q12.3) MUTATED   8 2
  DEL PEAK 14(5Q12.3) WILD-TYPE 4 4
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                           10                             8 
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                            2                             4 
$`DEL PEAK 14(5Q12.3) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO 
        0.26         0.53         3.48         3.68         4.08         3.32 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-LN-A4A2 
        3.16        30.71         7.10         0.13 

$`DEL PEAK 14(5Q12.3) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU 
        0.03         0.79         0.36        18.35         1.38        29.00 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                        30.71                         29.00 
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                        3.400                         1.085 
[1] "0.1 - 30.7 (3.4)" "0.0 - 29.0 (1.1)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 14(5Q12.3) MUTATED"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 14(5Q12.3) MUTATED"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 14(5Q12.3) MUTATED"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
[1] "hr=" "2"  
D37V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 14(5Q12.3) MUTATED          2        0         1         4
  DEL PEAK 14(5Q12.3) WILD-TYPE        0        1         2         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 14(5Q12.3) MUTATED            3          2          1
  DEL PEAK 14(5Q12.3) WILD-TYPE          2          1          0
D37V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 14(5Q12.3) MUTATED    3  3     7
  DEL PEAK 14(5Q12.3) WILD-TYPE  1  4     4
D37V4, multiclass
       clus
vv      DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE
  T1                              3                             1
  T2                              3                             4
  T3+T4                           7                             4
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 14(5Q12.3) MUTATED    4  6     3
  DEL PEAK 14(5Q12.3) WILD-TYPE  4  4     1
D37V5, multiclass
       clus
vv      DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE
  N0                              4                             4
  N1                              6                             4
  N2+N3                           3                             1
D37V6, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q12.3) MUTATED    3 10
  DEL PEAK 14(5Q12.3) WILD-TYPE  0  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.3) MUTATED      3   10
  DEL PEAK 14(5Q12.3) WILD-TYPE    0    9
        clus
vv       DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE
  FEMALE                           3                             0
  MALE                            10                             9
D37V7, continuous

Clustering(38) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 15(6P25.3) MUTATED   5 4
  DEL PEAK 15(6P25.3) WILD-TYPE 7 2
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                            9                             9 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                            4                             2 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         0.26         0.53        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-LN-A4A2 
        3.16         7.10         0.13 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS 
        0.79         0.36         3.48         3.68         4.08        30.71 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A9 
       29.00         7.43         0.07 

  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 
                        18.35                         30.71 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         1.38                          3.68 
[1] "0.0 - 18.4 (1.4)" "0.1 - 30.7 (3.7)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
[1] "hr=" "3.4"
D38V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 15(6P25.3) MUTATED          1        0         1         3
  DEL PEAK 15(6P25.3) WILD-TYPE        1        1         2         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 15(6P25.3) MUTATED            2          1          1
  DEL PEAK 15(6P25.3) WILD-TYPE          3          2          0
D38V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 15(6P25.3) MUTATED    2  3     4
  DEL PEAK 15(6P25.3) WILD-TYPE  2  4     7
D38V4, multiclass
       clus
vv      DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T1                              2                             2
  T2                              3                             4
  T3+T4                           4                             7
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 15(6P25.3) MUTATED    2  5     2
  DEL PEAK 15(6P25.3) WILD-TYPE  6  5     2
D38V5, multiclass
       clus
vv      DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                              2                             6
  N1                              5                             5
  N2+N3                           2                             2
D38V6, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED    1  8
  DEL PEAK 15(6P25.3) WILD-TYPE  2 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      1    8
  DEL PEAK 15(6P25.3) WILD-TYPE    2   11
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                           1                             2
  MALE                             8                            11
D38V7, continuous

Clustering(39) Variable = DEL PEAK 16(6Q16.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 16(6Q16.1) MUTATED    2  2
  DEL PEAK 16(6Q16.1) WILD-TYPE 10  4
  DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE 
                            4                            14 
  DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE 
                            2                             4 
$`DEL PEAK 16(6Q16.1) MUTATED`
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OR TCGA-LN-A4A2 
        3.68        18.35         3.16         0.13 

$`DEL PEAK 16(6Q16.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE 
        0.03         0.26         0.53         0.79         0.36         3.48 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        4.08         3.32         1.38        30.71        29.00         7.10 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE 
                        18.35                         30.71 
  DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE 
                         3.42                          2.35 
[1] "0.1 - 18.4 (3.4)" "0.0 - 30.7 (2.3)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 16(6Q16.1) MUTATED" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 16(6Q16.1) MUTATED" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 16(6Q16.1) WILD-TYPE"   "DEL PEAK 16(6Q16.1) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 16(6Q16.1) MUTATED" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 16(6Q16.1) MUTATED" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 16(6Q16.1) MUTATED" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 16(6Q16.1) WILD-TYPE"   "DEL PEAK 16(6Q16.1) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 16(6Q16.1) MUTATED" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 16(6Q16.1) MUTATED" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 16(6Q16.1) MUTATED" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 16(6Q16.1) WILD-TYPE"   "DEL PEAK 16(6Q16.1) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 16(6Q16.1) MUTATED" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
[1] "hr=" "1.4"
D39V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 16(6Q16.1) MUTATED          1        0         1         2
  DEL PEAK 16(6Q16.1) WILD-TYPE        1        1         2         5
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 16(6Q16.1) MUTATED            0          0          0
  DEL PEAK 16(6Q16.1) WILD-TYPE          5          3          1
D39V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 16(6Q16.1) MUTATED    3  0     1
  DEL PEAK 16(6Q16.1) WILD-TYPE  1  7    10
D39V4, multiclass
       clus
vv      DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE
  T1                              3                             1
  T2                              0                             7
  T3+T4                           1                            10
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 16(6Q16.1) MUTATED    2  2     0
  DEL PEAK 16(6Q16.1) WILD-TYPE  6  8     4
D39V5, multiclass
       clus
vv      DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE
  N0                              2                             6
  N1                              2                             8
  N2+N3                           0                             4
D39V6, binary
                               cls
clus                             0  1
  DEL PEAK 16(6Q16.1) MUTATED    0  4
  DEL PEAK 16(6Q16.1) WILD-TYPE  3 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.1) MUTATED      0    4
  DEL PEAK 16(6Q16.1) WILD-TYPE    3   15
        clus
vv       DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE
  FEMALE                           0                             3
  MALE                             4                            15
D39V7, continuous
[1] "Remove cluster labels:"      "DEL PEAK 16(6Q16.1) MUTATED"
clus
  DEL PEAK 16(6Q16.1) MUTATED DEL PEAK 16(6Q16.1) WILD-TYPE 
                            1                            13 
                   TCGA-IG-A3Y9                    TCGA-IG-A3YA 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A50L 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-IG-A5B8                    TCGA-L5-A4OE 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4OO 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OU 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 16(6Q16.1) WILD-TYPE" "DEL PEAK 16(6Q16.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"DEL PEAK 16(6Q16.1) WILD-TYPE" 

Clustering(40) Variable = DEL PEAK 17(7Q31.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 17(7Q31.1) MUTATED   4 2
  DEL PEAK 17(7Q31.1) WILD-TYPE 8 4
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            6                            12 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            2                             4 
$`DEL PEAK 17(7Q31.1) MUTATED`
TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
        0.26         0.79         3.68         4.08         3.16        29.00 

$`DEL PEAK 17(7Q31.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.53         0.36         3.48        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        1.38        30.71         7.10         7.43         0.13         0.07 

  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                         0.26                          0.03 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                        29.00                         30.71 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                         3.42                          2.35 
[1] "0.3 - 29.0 (3.4)" "0.0 - 30.7 (2.3)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 17(7Q31.1) MUTATED"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 17(7Q31.1) MUTATED"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 17(7Q31.1) MUTATED"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
[1] "hr=" "1"  
D40V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 17(7Q31.1) MUTATED          2        1         1         2
  DEL PEAK 17(7Q31.1) WILD-TYPE        0        0         2         5
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 17(7Q31.1) MUTATED            2          1          0
  DEL PEAK 17(7Q31.1) WILD-TYPE          3          2          1
D40V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 17(7Q31.1) MUTATED    3  1     5
  DEL PEAK 17(7Q31.1) WILD-TYPE  1  6     6
D40V4, multiclass
       clus
vv      DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  T1                              3                             1
  T2                              1                             6
  T3+T4                           5                             6
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 17(7Q31.1) MUTATED    5  3     1
  DEL PEAK 17(7Q31.1) WILD-TYPE  3  7     3
D40V5, multiclass
       clus
vv      DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  N0                              5                             3
  N1                              3                             7
  N2+N3                           1                             3
D40V6, binary
                               cls
clus                             0  1
  DEL PEAK 17(7Q31.1) MUTATED    1  8
  DEL PEAK 17(7Q31.1) WILD-TYPE  2 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      1    8
  DEL PEAK 17(7Q31.1) WILD-TYPE    2   11
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  FEMALE                           1                             2
  MALE                             8                            11
D40V7, continuous

Clustering(41) Variable = DEL PEAK 18(7Q36.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 18(7Q36.2) MUTATED   4 3
  DEL PEAK 18(7Q36.2) WILD-TYPE 8 3
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                            7                            11 
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                            3                             3 
$`DEL PEAK 18(7Q36.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR 
        0.03         0.79         3.68         4.08        18.35         3.16 
TCGA-L5-A4OU 
       29.00 

$`DEL PEAK 18(7Q36.2) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         0.53         0.36         3.48         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       30.71         7.10         7.43         0.13         0.07 

  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                        29.00                         30.71 
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                         3.68                          1.38 
[1] "0.0 - 29.0 (3.7)" "0.1 - 30.7 (1.4)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 18(7Q36.2) MUTATED"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 18(7Q36.2) MUTATED"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 18(7Q36.2) MUTATED"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
[1] "hr=" "1"  
D41V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 18(7Q36.2) MUTATED          2        1         1         4
  DEL PEAK 18(7Q36.2) WILD-TYPE        0        0         2         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 18(7Q36.2) MUTATED            1          0          0
  DEL PEAK 18(7Q36.2) WILD-TYPE          4          3          1
D41V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 18(7Q36.2) MUTATED    4  2     3
  DEL PEAK 18(7Q36.2) WILD-TYPE  0  5     8
D41V4, multiclass
       clus
vv      DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE
  T1                              4                             0
  T2                              2                             5
  T3+T4                           3                             8
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 18(7Q36.2) MUTATED    5  4     0
  DEL PEAK 18(7Q36.2) WILD-TYPE  3  6     4
D41V5, multiclass
       clus
vv      DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE
  N0                              5                             3
  N1                              4                             6
  N2+N3                           0                             4
D41V6, binary
                               cls
clus                             0  1
  DEL PEAK 18(7Q36.2) MUTATED    1  8
  DEL PEAK 18(7Q36.2) WILD-TYPE  2 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q36.2) MUTATED      1    8
  DEL PEAK 18(7Q36.2) WILD-TYPE    2   11
        clus
vv       DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE
  FEMALE                           1                             2
  MALE                             8                            11
D41V7, continuous

Clustering(42) Variable = DEL PEAK 19(8P23.2) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 19(8P23.2) MUTATED   7 2
  DEL PEAK 19(8P23.2) WILD-TYPE 5 4
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                            9                             9 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                            2                             4 
$`DEL PEAK 19(8P23.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.26         0.53         0.79         3.48         3.68 
TCGA-L5-A4OO TCGA-L5-A4OX TCGA-LN-A4A2 
        3.32         7.43         0.13 

$`DEL PEAK 19(8P23.2) WILD-TYPE`
TCGA-IG-A625 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        0.36         4.08        18.35         1.38         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
       29.00         7.10         0.07 

  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                         7.43                         30.71 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                         0.79                          4.08 
[1] "0.0 - 7.4 (0.8)"  "0.1 - 30.7 (4.1)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 19(8P23.2) WILD-TYPE"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 19(8P23.2) MUTATED" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 19(8P23.2) WILD-TYPE"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 19(8P23.2) WILD-TYPE"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 19(8P23.2) MUTATED" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 19(8P23.2) WILD-TYPE"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 19(8P23.2) MUTATED" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 19(8P23.2) WILD-TYPE"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 19(8P23.2) WILD-TYPE"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 19(8P23.2) MUTATED" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
"DEL PEAK 19(8P23.2) WILD-TYPE"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 19(8P23.2) MUTATED" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
"DEL PEAK 19(8P23.2) WILD-TYPE"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 19(8P23.2) WILD-TYPE"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 19(8P23.2) MUTATED" "DEL PEAK 19(8P23.2) WILD-TYPE" 
[1] "hr=" "1.4"
D42V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 19(8P23.2) MUTATED          0        1         1         4
  DEL PEAK 19(8P23.2) WILD-TYPE        2        0         2         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 19(8P23.2) MUTATED            3          2          1
  DEL PEAK 19(8P23.2) WILD-TYPE          2          1          0
D42V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 19(8P23.2) MUTATED    1  3     8
  DEL PEAK 19(8P23.2) WILD-TYPE  3  4     3
D42V4, multiclass
       clus
vv      DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  T1                              1                             3
  T2                              3                             4
  T3+T4                           8                             3
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 19(8P23.2) MUTATED    3  6     3
  DEL PEAK 19(8P23.2) WILD-TYPE  5  4     1
D42V5, multiclass
       clus
vv      DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  N0                              3                             5
  N1                              6                             4
  N2+N3                           3                             1
D42V6, binary
                               cls
clus                             0  1
  DEL PEAK 19(8P23.2) MUTATED    0 12
  DEL PEAK 19(8P23.2) WILD-TYPE  3  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.2) MUTATED      0   12
  DEL PEAK 19(8P23.2) WILD-TYPE    3    7
        clus
vv       DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  FEMALE                           0                             3
  MALE                            12                             7
D42V7, continuous

Clustering(43) Variable = DEL PEAK 20(9P21.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 20(9P21.3) MUTATED   11  4
  DEL PEAK 20(9P21.3) WILD-TYPE  1  2
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                           15                             3 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                            4                             2 
$`DEL PEAK 20(9P21.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OF 
        0.03         0.26         0.53         0.79         0.36         3.68 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        4.08        18.35         3.32        30.71        29.00         7.10 
TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.43         0.13         0.07 

$`DEL PEAK 20(9P21.3) WILD-TYPE`
TCGA-L5-A4OE TCGA-L5-A4OQ TCGA-L5-A4OR 
        3.48         1.38         3.16 

  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                         0.03                          1.38 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                        30.71                          3.48 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                         3.32                          3.16 
[1] "0.0 - 30.7 (3.3)" "1.4 - 3.5 (3.2)" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 20(9P21.3) WILD-TYPE" "DEL PEAK 20(9P21.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 20(9P21.3) WILD-TYPE" "DEL PEAK 20(9P21.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) WILD-TYPE" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 20(9P21.3) WILD-TYPE" "DEL PEAK 20(9P21.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
[1] "hr=" "6.4"
D43V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 20(9P21.3) MUTATED          1        1         3         7
  DEL PEAK 20(9P21.3) WILD-TYPE        1        0         0         0
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 20(9P21.3) MUTATED            4          2          1
  DEL PEAK 20(9P21.3) WILD-TYPE          1          1          0
D43V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 20(9P21.3) MUTATED    3  6    10
  DEL PEAK 20(9P21.3) WILD-TYPE  1  1     1
D43V4, multiclass
       clus
vv      DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  T1                              3                             1
  T2                              6                             1
  T3+T4                          10                             1
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 20(9P21.3) MUTATED    7  9     3
  DEL PEAK 20(9P21.3) WILD-TYPE  1  1     1
D43V5, multiclass
       clus
vv      DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  N0                              7                             1
  N1                              9                             1
  N2+N3                           3                             1
D43V6, binary
                               cls
clus                             0  1
  DEL PEAK 20(9P21.3) MUTATED    3 16
  DEL PEAK 20(9P21.3) WILD-TYPE  0  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9P21.3) MUTATED      3   16
  DEL PEAK 20(9P21.3) WILD-TYPE    0    3
        clus
vv       DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  FEMALE                           3                             0
  MALE                            16                             3
D43V7, continuous
[1] "Remove cluster labels:"        "DEL PEAK 20(9P21.3) WILD-TYPE"
clus
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                           12                             2 
                 TCGA-IG-A3Y9                  TCGA-IG-A3YA 
"DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) MUTATED" 
                 TCGA-IG-A4P3                  TCGA-IG-A50L 
"DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) MUTATED" 
                 TCGA-IG-A5B8                  TCGA-L5-A4OM 
"DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) MUTATED" 
                 TCGA-L5-A4ON                  TCGA-L5-A4OO 
"DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) MUTATED" 
                 TCGA-L5-A4OU                  TCGA-L5-A4OW 
"DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) MUTATED" 
                 TCGA-L5-A4OX                  TCGA-LN-A4A9 
"DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) MUTATED" 

Clustering(44) Variable = DEL PEAK 21(10P11.21) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 21(10P11.21) MUTATED   4 1
  DEL PEAK 21(10P11.21) WILD-TYPE 8 5
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                              5                              13 
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                              1                               5 
$`DEL PEAK 21(10P11.21) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-LN-A4A9 
        0.03         0.53         0.79         3.48         0.07 

$`DEL PEAK 21(10P11.21) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         0.36         3.68         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        30.71        29.00         7.10         7.43 
TCGA-LN-A4A2 
        0.13 

  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                           0.03                            0.13 
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                           3.48                           30.71 
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                           0.53                            3.68 
[1] "0.0 - 3.5 (0.5)"  "0.1 - 30.7 (3.7)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 21(10P11.21) MUTATED" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 21(10P11.21) MUTATED"   "DEL PEAK 21(10P11.21) MUTATED" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 21(10P11.21) WILD-TYPE"   "DEL PEAK 21(10P11.21) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
"DEL PEAK 21(10P11.21) WILD-TYPE"   "DEL PEAK 21(10P11.21) MUTATED" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 21(10P11.21) MUTATED" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 21(10P11.21) MUTATED"   "DEL PEAK 21(10P11.21) MUTATED" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 21(10P11.21) WILD-TYPE"   "DEL PEAK 21(10P11.21) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
"DEL PEAK 21(10P11.21) WILD-TYPE"   "DEL PEAK 21(10P11.21) MUTATED" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 21(10P11.21) MUTATED" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 21(10P11.21) MUTATED"   "DEL PEAK 21(10P11.21) MUTATED" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 21(10P11.21) WILD-TYPE"   "DEL PEAK 21(10P11.21) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
"DEL PEAK 21(10P11.21) WILD-TYPE"   "DEL PEAK 21(10P11.21) MUTATED" 
[1] "hr=" "3.8"
D44V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 21(10P11.21) MUTATED          0        1         1         1
  DEL PEAK 21(10P11.21) WILD-TYPE        2        0         2         6
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 21(10P11.21) MUTATED            2          1          0
  DEL PEAK 21(10P11.21) WILD-TYPE          3          2          1
D44V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 21(10P11.21) MUTATED    0  2     4
  DEL PEAK 21(10P11.21) WILD-TYPE  4  5     7
D44V4, multiclass
       clus
vv      DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE
  T1                                0                               4
  T2                                2                               5
  T3+T4                             4                               7
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 21(10P11.21) MUTATED    3  2     1
  DEL PEAK 21(10P11.21) WILD-TYPE  5  8     3
D44V5, multiclass
       clus
vv      DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE
  N0                                3                               5
  N1                                2                               8
  N2+N3                             1                               3
D44V6, binary
                                 cls
clus                               0  1
  DEL PEAK 21(10P11.21) MUTATED    0  6
  DEL PEAK 21(10P11.21) WILD-TYPE  3 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(10P11.21) MUTATED      0    6
  DEL PEAK 21(10P11.21) WILD-TYPE    3   13
        clus
vv       DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE
  FEMALE                             0                               3
  MALE                               6                              13
D44V7, continuous

Clustering(45) Variable = DEL PEAK 22(10Q23.31) MUTATION ANALYSIS
D45V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 22(10Q23.31) MUTATED   5 2
  DEL PEAK 22(10Q23.31) WILD-TYPE 7 4
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              7                              11 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              2                               4 
$`DEL PEAK 22(10Q23.31) MUTATED`
TCGA-IG-A50L TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        0.53         3.48         3.32         3.16        30.71         7.10 
TCGA-LN-A4A2 
        0.13 

$`DEL PEAK 22(10Q23.31) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OM 
        0.03         0.26         0.79         0.36         3.68         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A9 
       18.35         1.38        29.00         7.43         0.07 

  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                           0.13                            0.03 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                          30.71                           29.00 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                           3.32                            1.38 
[1] "0.1 - 30.7 (3.3)" "0.0 - 29.0 (1.4)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
[1] "hr=" "1.3"
D45V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 22(10Q23.31) MUTATED          1        0         1         2
  DEL PEAK 22(10Q23.31) WILD-TYPE        1        1         2         5
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 22(10Q23.31) MUTATED            3          1          1
  DEL PEAK 22(10Q23.31) WILD-TYPE          2          2          0
D45V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 22(10Q23.31) MUTATED    1  2     6
  DEL PEAK 22(10Q23.31) WILD-TYPE  3  5     5
D45V4, multiclass
       clus
vv      DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  T1                                1                               3
  T2                                2                               5
  T3+T4                             6                               5
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 22(10Q23.31) MUTATED    3  4     2
  DEL PEAK 22(10Q23.31) WILD-TYPE  5  6     2
D45V5, multiclass
       clus
vv      DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  N0                                3                               5
  N1                                4                               6
  N2+N3                             2                               2
D45V6, binary
                                 cls
clus                               0  1
  DEL PEAK 22(10Q23.31) MUTATED    2  7
  DEL PEAK 22(10Q23.31) WILD-TYPE  1 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      2    7
  DEL PEAK 22(10Q23.31) WILD-TYPE    1   12
        clus
vv       DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  FEMALE                             2                               1
  MALE                               7                              12
D45V7, continuous

Clustering(46) Variable = DEL PEAK 23(11P15.4) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 23(11P15.4) MUTATED   3 1
  DEL PEAK 23(11P15.4) WILD-TYPE 9 5
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                             4                             14 
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                             1                              5 
$`DEL PEAK 23(11P15.4) MUTATED`
TCGA-IG-A50L TCGA-L5-A4OO TCGA-L5-A4OR TCGA-LN-A4A2 
        0.53         3.32         3.16         0.13 

$`DEL PEAK 23(11P15.4) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.26         0.79         0.36         3.48         3.68 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        4.08        18.35         1.38        30.71        29.00         7.10 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                          0.13                           0.03 
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                          3.32                          30.71 
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                         1.845                          3.580 
[1] "0.1 - 3.3 (1.8)"  "0.0 - 30.7 (3.6)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 23(11P15.4) WILD-TYPE"   "DEL PEAK 23(11P15.4) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 23(11P15.4) WILD-TYPE"   "DEL PEAK 23(11P15.4) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 23(11P15.4) WILD-TYPE"   "DEL PEAK 23(11P15.4) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 23(11P15.4) WILD-TYPE"   "DEL PEAK 23(11P15.4) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 23(11P15.4) WILD-TYPE"   "DEL PEAK 23(11P15.4) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 23(11P15.4) WILD-TYPE"   "DEL PEAK 23(11P15.4) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
[1] "hr=" "2.2"
D46V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 23(11P15.4) MUTATED          1        0         1         0
  DEL PEAK 23(11P15.4) WILD-TYPE        1        1         2         7
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 23(11P15.4) MUTATED            3          0          1
  DEL PEAK 23(11P15.4) WILD-TYPE          2          3          0
D46V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 23(11P15.4) MUTATED    1  0     5
  DEL PEAK 23(11P15.4) WILD-TYPE  3  7     6
D46V4, multiclass
       clus
vv      DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE
  T1                               1                              3
  T2                               0                              7
  T3+T4                            5                              6
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 23(11P15.4) MUTATED    3  2     1
  DEL PEAK 23(11P15.4) WILD-TYPE  5  8     3
D46V5, multiclass
       clus
vv      DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE
  N0                               3                              5
  N1                               2                              8
  N2+N3                            1                              3
D46V6, binary
                                cls
clus                              0  1
  DEL PEAK 23(11P15.4) MUTATED    0  6
  DEL PEAK 23(11P15.4) WILD-TYPE  3 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.4) MUTATED      0    6
  DEL PEAK 23(11P15.4) WILD-TYPE    3   13
        clus
vv       DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE
  FEMALE                            0                              3
  MALE                              6                             13
D46V7, continuous

Clustering(47) Variable = DEL PEAK 24(11Q24.3) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 24(11Q24.3) MUTATED   7 1
  DEL PEAK 24(11Q24.3) WILD-TYPE 5 5
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                             8                             10 
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                             1                              5 
$`DEL PEAK 24(11Q24.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         0.26         3.68         4.08         3.32         3.16 
TCGA-L5-A4OU TCGA-LN-A4A2 
       29.00         0.13 

$`DEL PEAK 24(11Q24.3) WILD-TYPE`
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.53         0.79         0.36         3.48        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
       30.71         7.10         7.43         0.07 

  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                          3.24                           2.43 
[1] "0.0 - 29.0 (3.2)" "0.1 - 30.7 (2.4)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 24(11Q24.3) MUTATED"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 24(11Q24.3) WILD-TYPE" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 24(11Q24.3) WILD-TYPE" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 24(11Q24.3) MUTATED"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 24(11Q24.3) WILD-TYPE" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 24(11Q24.3) MUTATED"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 24(11Q24.3) WILD-TYPE" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 24(11Q24.3) WILD-TYPE" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 24(11Q24.3) MUTATED"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 24(11Q24.3) WILD-TYPE" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 24(11Q24.3) MUTATED"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 24(11Q24.3) WILD-TYPE" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 24(11Q24.3) WILD-TYPE" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 24(11Q24.3) MUTATED"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 24(11Q24.3) WILD-TYPE" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
[1] "hr=" "2.9"
D47V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 24(11Q24.3) MUTATED          2        0         2         3
  DEL PEAK 24(11Q24.3) WILD-TYPE        0        1         1         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 24(11Q24.3) MUTATED            0          1          1
  DEL PEAK 24(11Q24.3) WILD-TYPE          5          2          0
D47V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 24(11Q24.3) MUTATED    3  2     4
  DEL PEAK 24(11Q24.3) WILD-TYPE  1  5     7
D47V4, multiclass
       clus
vv      DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE
  T1                               3                              1
  T2                               2                              5
  T3+T4                            4                              7
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 24(11Q24.3) MUTATED    4  3     2
  DEL PEAK 24(11Q24.3) WILD-TYPE  4  7     2
D47V5, multiclass
       clus
vv      DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE
  N0                               4                              4
  N1                               3                              7
  N2+N3                            2                              2
D47V6, binary
                                cls
clus                              0  1
  DEL PEAK 24(11Q24.3) MUTATED    1  8
  DEL PEAK 24(11Q24.3) WILD-TYPE  2 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11Q24.3) MUTATED      1    8
  DEL PEAK 24(11Q24.3) WILD-TYPE    2   11
        clus
vv       DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE
  FEMALE                            1                              2
  MALE                              8                             11
D47V7, continuous

Clustering(48) Variable = DEL PEAK 25(12Q23.1) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 25(12Q23.1) MUTATED   3 2
  DEL PEAK 25(12Q23.1) WILD-TYPE 9 4
  DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE 
                             5                             13 
  DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE 
                             2                              4 
$`DEL PEAK 25(12Q23.1) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A4OO TCGA-L5-A4OS TCGA-L5-A4OW 
        0.03         0.79         3.32        30.71         7.10 

$`DEL PEAK 25(12Q23.1) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM 
        0.26         0.53         0.36         3.48         3.68         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 
       18.35         1.38         3.16        29.00         7.43         0.13 
TCGA-LN-A4A9 
        0.07 

  DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE 
                         30.71                          29.00 
  DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE 
                          3.32                           3.16 
[1] "0.0 - 30.7 (3.3)" "0.1 - 29.0 (3.2)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 25(12Q23.1) MUTATED" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 25(12Q23.1) WILD-TYPE"   "DEL PEAK 25(12Q23.1) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 25(12Q23.1) WILD-TYPE"   "DEL PEAK 25(12Q23.1) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 25(12Q23.1) MUTATED" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 25(12Q23.1) MUTATED" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 25(12Q23.1) MUTATED" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 25(12Q23.1) WILD-TYPE"   "DEL PEAK 25(12Q23.1) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 25(12Q23.1) WILD-TYPE"   "DEL PEAK 25(12Q23.1) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 25(12Q23.1) MUTATED" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 25(12Q23.1) MUTATED" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 25(12Q23.1) MUTATED" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 25(12Q23.1) WILD-TYPE"   "DEL PEAK 25(12Q23.1) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 25(12Q23.1) WILD-TYPE"   "DEL PEAK 25(12Q23.1) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 25(12Q23.1) MUTATED" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 25(12Q23.1) MUTATED" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 25(12Q23.1) WILD-TYPE" "DEL PEAK 25(12Q23.1) WILD-TYPE" 
[1] "hr=" "1.1"
D48V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 25(12Q23.1) MUTATED          0        1         0         3
  DEL PEAK 25(12Q23.1) WILD-TYPE        2        0         3         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 25(12Q23.1) MUTATED            1          0          1
  DEL PEAK 25(12Q23.1) WILD-TYPE          4          3          0
D48V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 25(12Q23.1) MUTATED    0  3     3
  DEL PEAK 25(12Q23.1) WILD-TYPE  4  4     8
D48V4, multiclass
       clus
vv      DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE
  T1                               0                              4
  T2                               3                              4
  T3+T4                            3                              8
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 25(12Q23.1) MUTATED    1  4     1
  DEL PEAK 25(12Q23.1) WILD-TYPE  7  6     3
D48V5, multiclass
       clus
vv      DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE
  N0                               1                              7
  N1                               4                              6
  N2+N3                            1                              3
D48V6, binary
                                cls
clus                              0  1
  DEL PEAK 25(12Q23.1) MUTATED    2  4
  DEL PEAK 25(12Q23.1) WILD-TYPE  1 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12Q23.1) MUTATED      2    4
  DEL PEAK 25(12Q23.1) WILD-TYPE    1   15
        clus
vv       DEL PEAK 25(12Q23.1) MUTATED DEL PEAK 25(12Q23.1) WILD-TYPE
  FEMALE                            2                              1
  MALE                              4                             15
D48V7, continuous

Clustering(49) Variable = DEL PEAK 26(13Q12.11) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 26(13Q12.11) MUTATED   6 2
  DEL PEAK 26(13Q12.11) WILD-TYPE 6 4
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                              8                              10 
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                              2                               4 
$`DEL PEAK 26(13Q12.11) MUTATED`
TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
        0.26         0.79         3.68         4.08         3.16        29.00 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

$`DEL PEAK 26(13Q12.11) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.53         0.36         3.48        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        30.71         7.10         7.43 

  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                          29.00                           30.71 
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                          1.975                           3.400 
[1] "0.1 - 29.0 (2.0)" "0.0 - 30.7 (3.4)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
  "DEL PEAK 26(13Q12.11) MUTATED"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "DEL PEAK 26(13Q12.11) MUTATED"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
  "DEL PEAK 26(13Q12.11) MUTATED"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "DEL PEAK 26(13Q12.11) MUTATED"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
  "DEL PEAK 26(13Q12.11) MUTATED"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "DEL PEAK 26(13Q12.11) MUTATED"   "DEL PEAK 26(13Q12.11) MUTATED" 
[1] "hr=" "1"  
D49V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 26(13Q12.11) MUTATED          2        1         3         2
  DEL PEAK 26(13Q12.11) WILD-TYPE        0        0         0         5
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 26(13Q12.11) MUTATED            3          1          0
  DEL PEAK 26(13Q12.11) WILD-TYPE          2          2          1
D49V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 26(13Q12.11) MUTATED    3  2     7
  DEL PEAK 26(13Q12.11) WILD-TYPE  1  5     4
D49V4, multiclass
       clus
vv      DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE
  T1                                3                               1
  T2                                2                               5
  T3+T4                             7                               4
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 26(13Q12.11) MUTATED    8  3     1
  DEL PEAK 26(13Q12.11) WILD-TYPE  0  7     3
D49V5, multiclass
       clus
vv      DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE
  N0                                8                               0
  N1                                3                               7
  N2+N3                             1                               3
D49V6, binary
                                 cls
clus                               0  1
  DEL PEAK 26(13Q12.11) MUTATED    1 11
  DEL PEAK 26(13Q12.11) WILD-TYPE  2  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(13Q12.11) MUTATED      1   11
  DEL PEAK 26(13Q12.11) WILD-TYPE    2    8
        clus
vv       DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE
  FEMALE                             1                               2
  MALE                              11                               8
D49V7, continuous

Clustering(50) Variable = DEL PEAK 27(13Q14.2) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 27(13Q14.2) MUTATED   8 1
  DEL PEAK 27(13Q14.2) WILD-TYPE 4 5
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                             9                              9 
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                             1                              5 
$`DEL PEAK 27(13Q14.2) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR 
        0.26         0.53         3.48         3.68         4.08         3.16 
TCGA-L5-A4OU TCGA-LN-A4A2 TCGA-LN-A4A9 
       29.00         0.13         0.07 

$`DEL PEAK 27(13Q14.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         0.79         0.36        18.35         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
       30.71         7.10         7.43 

  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE 
                          3.16                           3.32 
[1] "0.1 - 29.0 (3.2)" "0.0 - 30.7 (3.3)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 27(13Q14.2) MUTATED" "DEL PEAK 27(13Q14.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 27(13Q14.2) MUTATED"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 27(13Q14.2) WILD-TYPE" "DEL PEAK 27(13Q14.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 27(13Q14.2) WILD-TYPE" "DEL PEAK 27(13Q14.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 27(13Q14.2) MUTATED"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 27(13Q14.2) MUTATED" "DEL PEAK 27(13Q14.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 27(13Q14.2) MUTATED"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 27(13Q14.2) WILD-TYPE" "DEL PEAK 27(13Q14.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 27(13Q14.2) WILD-TYPE" "DEL PEAK 27(13Q14.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 27(13Q14.2) MUTATED"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 27(13Q14.2) MUTATED" "DEL PEAK 27(13Q14.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 27(13Q14.2) MUTATED"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 27(13Q14.2) WILD-TYPE" "DEL PEAK 27(13Q14.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 27(13Q14.2) WILD-TYPE"   "DEL PEAK 27(13Q14.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 27(13Q14.2) WILD-TYPE" "DEL PEAK 27(13Q14.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 27(13Q14.2) MUTATED"   "DEL PEAK 27(13Q14.2) MUTATED" 
[1] "hr=" "2.9"
D50V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 27(13Q14.2) MUTATED          2        0         3         2
  DEL PEAK 27(13Q14.2) WILD-TYPE        0        1         0         5
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 27(13Q14.2) MUTATED            4          2          0
  DEL PEAK 27(13Q14.2) WILD-TYPE          1          1          1
D50V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 27(13Q14.2) MUTATED    3  2     8
  DEL PEAK 27(13Q14.2) WILD-TYPE  1  5     3
D50V4, multiclass
       clus
vv      DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE
  T1                               3                              1
  T2                               2                              5
  T3+T4                            8                              3
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 27(13Q14.2) MUTATED    7  4     2
  DEL PEAK 27(13Q14.2) WILD-TYPE  1  6     2
D50V5, multiclass
       clus
vv      DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE
  N0                               7                              1
  N1                               4                              6
  N2+N3                            2                              2
D50V6, binary
                                cls
clus                              0  1
  DEL PEAK 27(13Q14.2) MUTATED    1 12
  DEL PEAK 27(13Q14.2) WILD-TYPE  2  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(13Q14.2) MUTATED      1   12
  DEL PEAK 27(13Q14.2) WILD-TYPE    2    7
        clus
vv       DEL PEAK 27(13Q14.2) MUTATED DEL PEAK 27(13Q14.2) WILD-TYPE
  FEMALE                            1                              2
  MALE                             12                              7
D50V7, continuous

Clustering(51) Variable = DEL PEAK 28(15Q11.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 28(15Q11.2) MUTATED   5 0
  DEL PEAK 28(15Q11.2) WILD-TYPE 7 6
  DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE 
                             5                             13 
  DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE 
                             0                              6 
$`DEL PEAK 28(15Q11.2) MUTATED`
TCGA-IG-A4QS TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OU 
        0.26         0.36         3.48         4.08        29.00 

$`DEL PEAK 28(15Q11.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.53         0.79         3.68        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38         3.16        30.71         7.10         7.43         0.13 
TCGA-LN-A4A9 
        0.07 

  DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE 
                          3.48                           3.16 
[1] "0.3 - 29.0 (3.5)" "0.0 - 30.7 (3.2)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 28(15Q11.2) WILD-TYPE"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "DEL PEAK 28(15Q11.2) MUTATED"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 28(15Q11.2) WILD-TYPE"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 28(15Q11.2) WILD-TYPE"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 28(15Q11.2) WILD-TYPE"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "DEL PEAK 28(15Q11.2) MUTATED"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 28(15Q11.2) WILD-TYPE"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 28(15Q11.2) WILD-TYPE"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 28(15Q11.2) WILD-TYPE"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
  "DEL PEAK 28(15Q11.2) MUTATED"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 28(15Q11.2) WILD-TYPE"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 28(15Q11.2) WILD-TYPE"   "DEL PEAK 28(15Q11.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 28(15Q11.2) WILD-TYPE" "DEL PEAK 28(15Q11.2) WILD-TYPE" 
[1] "hr="     "8.2e+08"
D51V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 28(15Q11.2) MUTATED          1        0         1         0
  DEL PEAK 28(15Q11.2) WILD-TYPE        1        1         2         7
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 28(15Q11.2) MUTATED            0          3          0
  DEL PEAK 28(15Q11.2) WILD-TYPE          5          0          1
D51V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 28(15Q11.2) MUTATED    1  0     4
  DEL PEAK 28(15Q11.2) WILD-TYPE  3  7     7
D51V4, multiclass
       clus
vv      DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE
  T1                               1                              3
  T2                               0                              7
  T3+T4                            4                              7
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 28(15Q11.2) MUTATED    2  0     3
  DEL PEAK 28(15Q11.2) WILD-TYPE  6 10     1
D51V5, multiclass
       clus
vv      DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE
  N0                               2                              6
  N1                               0                             10
  N2+N3                            3                              1
D51V6, binary
                                cls
clus                              0  1
  DEL PEAK 28(15Q11.2) MUTATED    1  4
  DEL PEAK 28(15Q11.2) WILD-TYPE  2 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q11.2) MUTATED      1    4
  DEL PEAK 28(15Q11.2) WILD-TYPE    2   15
        clus
vv       DEL PEAK 28(15Q11.2) MUTATED DEL PEAK 28(15Q11.2) WILD-TYPE
  FEMALE                            1                              2
  MALE                              4                             15
D51V7, continuous

Clustering(52) Variable = DEL PEAK 29(16Q23.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 29(16Q23.1) MUTATED   6 4
  DEL PEAK 29(16Q23.1) WILD-TYPE 6 2
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                            10                              8 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                             4                              2 
$`DEL PEAK 29(16Q23.1) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OR 
        0.26         0.53         3.48         3.68        18.35         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       30.71        29.00         7.10         7.43 

$`DEL PEAK 29(16Q23.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         0.79         0.36         4.08         3.32         1.38 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                         30.71                           4.08 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                         5.390                          0.575 
[1] "0.3 - 30.7 (5.4)" "0.0 - 4.1 (0.6)" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 29(16Q23.1) WILD-TYPE"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 29(16Q23.1) MUTATED" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 29(16Q23.1) WILD-TYPE"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 29(16Q23.1) MUTATED" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK 29(16Q23.1) MUTATED" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 29(16Q23.1) WILD-TYPE"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 29(16Q23.1) MUTATED"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 29(16Q23.1) MUTATED"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 29(16Q23.1) WILD-TYPE" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 29(16Q23.1) WILD-TYPE"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 29(16Q23.1) MUTATED" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 29(16Q23.1) WILD-TYPE"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 29(16Q23.1) MUTATED" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK 29(16Q23.1) MUTATED" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 29(16Q23.1) WILD-TYPE"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 29(16Q23.1) MUTATED"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 29(16Q23.1) MUTATED"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 29(16Q23.1) WILD-TYPE" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 29(16Q23.1) WILD-TYPE"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 29(16Q23.1) MUTATED" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 29(16Q23.1) WILD-TYPE"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 29(16Q23.1) MUTATED" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK 29(16Q23.1) MUTATED" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 29(16Q23.1) WILD-TYPE"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 29(16Q23.1) MUTATED"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 29(16Q23.1) MUTATED"   "DEL PEAK 29(16Q23.1) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 29(16Q23.1) WILD-TYPE" "DEL PEAK 29(16Q23.1) WILD-TYPE" 
[1] "hr=" "5.6"
D52V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 29(16Q23.1) MUTATED          1        0         1         5
  DEL PEAK 29(16Q23.1) WILD-TYPE        1        1         2         2
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 29(16Q23.1) MUTATED            1          2          0
  DEL PEAK 29(16Q23.1) WILD-TYPE          4          1          1
D52V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 29(16Q23.1) MUTATED    3  3     4
  DEL PEAK 29(16Q23.1) WILD-TYPE  1  4     7
D52V4, multiclass
       clus
vv      DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  T1                               3                              1
  T2                               3                              4
  T3+T4                            4                              7
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 29(16Q23.1) MUTATED    2  6     2
  DEL PEAK 29(16Q23.1) WILD-TYPE  6  4     2
D52V5, multiclass
       clus
vv      DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  N0                               2                              6
  N1                               6                              4
  N2+N3                            2                              2
D52V6, binary
                                cls
clus                              0  1
  DEL PEAK 29(16Q23.1) MUTATED    2  8
  DEL PEAK 29(16Q23.1) WILD-TYPE  1 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.1) MUTATED      2    8
  DEL PEAK 29(16Q23.1) WILD-TYPE    1   11
        clus
vv       DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  FEMALE                            2                              1
  MALE                              8                             11
D52V7, continuous

Clustering(53) Variable = DEL PEAK 30(17P11.2) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 30(17P11.2) MUTATED   6 3
  DEL PEAK 30(17P11.2) WILD-TYPE 6 3
  DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE 
                             9                              9 
  DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE 
                             3                              3 
$`DEL PEAK 30(17P11.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO 
        0.03         0.26         0.79         3.48         3.68         3.32 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       29.00         7.10         7.43 

$`DEL PEAK 30(17P11.2) WILD-TYPE`
TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.53         0.36         4.08        18.35         1.38         3.16 
TCGA-L5-A4OS TCGA-LN-A4A2 TCGA-LN-A4A9 
       30.71         0.13         0.07 

  DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE 
                          3.48                           1.38 
[1] "0.0 - 29.0 (3.5)" "0.1 - 30.7 (1.4)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 30(17P11.2) MUTATED"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 30(17P11.2) MUTATED" "DEL PEAK 30(17P11.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 30(17P11.2) WILD-TYPE" "DEL PEAK 30(17P11.2) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 30(17P11.2) MUTATED"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 30(17P11.2) WILD-TYPE" "DEL PEAK 30(17P11.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 30(17P11.2) MUTATED"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 30(17P11.2) MUTATED" "DEL PEAK 30(17P11.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 30(17P11.2) WILD-TYPE" "DEL PEAK 30(17P11.2) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 30(17P11.2) MUTATED"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 30(17P11.2) WILD-TYPE" "DEL PEAK 30(17P11.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 30(17P11.2) MUTATED"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 30(17P11.2) MUTATED" "DEL PEAK 30(17P11.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 30(17P11.2) WILD-TYPE" "DEL PEAK 30(17P11.2) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 30(17P11.2) WILD-TYPE"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 30(17P11.2) MUTATED"   "DEL PEAK 30(17P11.2) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 30(17P11.2) WILD-TYPE" "DEL PEAK 30(17P11.2) WILD-TYPE" 
[1] "hr=" "1.1"
D53V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 30(17P11.2) MUTATED          0        1         1         4
  DEL PEAK 30(17P11.2) WILD-TYPE        2        0         2         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 30(17P11.2) MUTATED            0          2          1
  DEL PEAK 30(17P11.2) WILD-TYPE          5          1          0
D53V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 30(17P11.2) MUTATED    1  3     5
  DEL PEAK 30(17P11.2) WILD-TYPE  3  4     6
D53V4, multiclass
       clus
vv      DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE
  T1                               1                              3
  T2                               3                              4
  T3+T4                            5                              6
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 30(17P11.2) MUTATED    2  4     3
  DEL PEAK 30(17P11.2) WILD-TYPE  6  6     1
D53V5, multiclass
       clus
vv      DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE
  N0                               2                              6
  N1                               4                              6
  N2+N3                            3                              1
D53V6, binary
                                cls
clus                              0  1
  DEL PEAK 30(17P11.2) MUTATED    1  8
  DEL PEAK 30(17P11.2) WILD-TYPE  2 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P11.2) MUTATED      1    8
  DEL PEAK 30(17P11.2) WILD-TYPE    2   11
        clus
vv       DEL PEAK 30(17P11.2) MUTATED DEL PEAK 30(17P11.2) WILD-TYPE
  FEMALE                            1                              2
  MALE                              8                             11
D53V7, continuous

Clustering(54) Variable = DEL PEAK 31(17Q25.3) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 31(17Q25.3) MUTATED    2  2
  DEL PEAK 31(17Q25.3) WILD-TYPE 10  4
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                             4                             14 
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                             2                              4 
$`DEL PEAK 31(17Q25.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A4OR TCGA-L5-A4OU 
        0.03         0.79         3.16        29.00 

$`DEL PEAK 31(17Q25.3) WILD-TYPE`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM 
        0.26         0.53         0.36         3.48         3.68         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
       18.35         3.32         1.38        30.71         7.10         7.43 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE 
                         1.975                          3.400 
[1] "0.0 - 29.0 (2.0)" "0.1 - 30.7 (3.4)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 31(17Q25.3) MUTATED" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 31(17Q25.3) WILD-TYPE"   "DEL PEAK 31(17Q25.3) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 31(17Q25.3) WILD-TYPE"   "DEL PEAK 31(17Q25.3) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 31(17Q25.3) WILD-TYPE"   "DEL PEAK 31(17Q25.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 31(17Q25.3) MUTATED" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 31(17Q25.3) WILD-TYPE"   "DEL PEAK 31(17Q25.3) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 31(17Q25.3) WILD-TYPE"   "DEL PEAK 31(17Q25.3) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 31(17Q25.3) WILD-TYPE"   "DEL PEAK 31(17Q25.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 31(17Q25.3) MUTATED" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 31(17Q25.3) WILD-TYPE"   "DEL PEAK 31(17Q25.3) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 31(17Q25.3) WILD-TYPE"   "DEL PEAK 31(17Q25.3) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 31(17Q25.3) WILD-TYPE"   "DEL PEAK 31(17Q25.3) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 31(17Q25.3) WILD-TYPE" "DEL PEAK 31(17Q25.3) WILD-TYPE" 
[1] "hr=" "1.6"
D54V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 31(17Q25.3) MUTATED          1        1         1         1
  DEL PEAK 31(17Q25.3) WILD-TYPE        1        0         2         6
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 31(17Q25.3) MUTATED            0          0          0
  DEL PEAK 31(17Q25.3) WILD-TYPE          5          3          1
D54V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 31(17Q25.3) MUTATED    1  1     2
  DEL PEAK 31(17Q25.3) WILD-TYPE  3  6     9
D54V4, multiclass
       clus
vv      DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE
  T1                               1                              3
  T2                               1                              6
  T3+T4                            2                              9
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 31(17Q25.3) MUTATED    3  1     0
  DEL PEAK 31(17Q25.3) WILD-TYPE  5  9     4
D54V5, multiclass
       clus
vv      DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE
  N0                               3                              5
  N1                               1                              9
  N2+N3                            0                              4
D54V6, binary
                                cls
clus                              0  1
  DEL PEAK 31(17Q25.3) MUTATED    0  4
  DEL PEAK 31(17Q25.3) WILD-TYPE  3 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17Q25.3) MUTATED      0    4
  DEL PEAK 31(17Q25.3) WILD-TYPE    3   15
        clus
vv       DEL PEAK 31(17Q25.3) MUTATED DEL PEAK 31(17Q25.3) WILD-TYPE
  FEMALE                            0                              3
  MALE                              4                             15
D54V7, continuous

Clustering(55) Variable = DEL PEAK 32(18Q12.2) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 32(18Q12.2) MUTATED   6 4
  DEL PEAK 32(18Q12.2) WILD-TYPE 6 2
  DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE 
                            10                              8 
  DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE 
                             4                              2 
$`DEL PEAK 32(18Q12.2) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO 
        0.26         0.53         0.79         3.48         3.68         3.32 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        29.00         7.10         7.43 

$`DEL PEAK 32(18Q12.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A625 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.03         0.36         4.08        18.35         1.38        30.71 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE 
                          3.40                           0.87 
[1] "0.3 - 29.0 (3.4)" "0.0 - 30.7 (0.9)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 32(18Q12.2) MUTATED"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 32(18Q12.2) MUTATED" "DEL PEAK 32(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 32(18Q12.2) MUTATED"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 32(18Q12.2) WILD-TYPE" "DEL PEAK 32(18Q12.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 32(18Q12.2) MUTATED"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 32(18Q12.2) MUTATED" "DEL PEAK 32(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 32(18Q12.2) MUTATED"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 32(18Q12.2) WILD-TYPE" "DEL PEAK 32(18Q12.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 32(18Q12.2) MUTATED"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 32(18Q12.2) MUTATED" "DEL PEAK 32(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 32(18Q12.2) WILD-TYPE"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 32(18Q12.2) MUTATED"   "DEL PEAK 32(18Q12.2) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 32(18Q12.2) WILD-TYPE" "DEL PEAK 32(18Q12.2) WILD-TYPE" 
[1] "hr=" "1.5"
D55V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 32(18Q12.2) MUTATED          1        1         1         3
  DEL PEAK 32(18Q12.2) WILD-TYPE        1        0         2         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 32(18Q12.2) MUTATED            3          2          1
  DEL PEAK 32(18Q12.2) WILD-TYPE          2          1          0
D55V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 32(18Q12.2) MUTATED    2  2     8
  DEL PEAK 32(18Q12.2) WILD-TYPE  2  5     3
D55V4, multiclass
       clus
vv      DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE
  T1                               2                              2
  T2                               2                              5
  T3+T4                            8                              3
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 32(18Q12.2) MUTATED    4  5     3
  DEL PEAK 32(18Q12.2) WILD-TYPE  4  5     1
D55V5, multiclass
       clus
vv      DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE
  N0                               4                              4
  N1                               5                              5
  N2+N3                            3                              1
D55V6, binary
                                cls
clus                              0  1
  DEL PEAK 32(18Q12.2) MUTATED    1 11
  DEL PEAK 32(18Q12.2) WILD-TYPE  2  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(18Q12.2) MUTATED      1   11
  DEL PEAK 32(18Q12.2) WILD-TYPE    2    8
        clus
vv       DEL PEAK 32(18Q12.2) MUTATED DEL PEAK 32(18Q12.2) WILD-TYPE
  FEMALE                            1                              2
  MALE                             11                              8
D55V7, continuous

Clustering(56) Variable = DEL PEAK 33(18Q21.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 33(18Q21.2) MUTATED   7 3
  DEL PEAK 33(18Q21.2) WILD-TYPE 5 3
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                            10                              8 
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                             3                              3 
$`DEL PEAK 33(18Q21.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.26         0.53         0.79         3.48         3.68 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         3.16        29.00         7.43 

$`DEL PEAK 33(18Q21.2) WILD-TYPE`
TCGA-IG-A625 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
        0.36         4.08        18.35         1.38        30.71         7.10 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                          3.24                           2.73 
[1] "0.0 - 29.0 (3.2)" "0.1 - 30.7 (2.7)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 33(18Q21.2) MUTATED"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 33(18Q21.2) MUTATED"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 33(18Q21.2) MUTATED" "DEL PEAK 33(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 33(18Q21.2) WILD-TYPE" "DEL PEAK 33(18Q21.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 33(18Q21.2) MUTATED"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 33(18Q21.2) MUTATED"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 33(18Q21.2) MUTATED" "DEL PEAK 33(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 33(18Q21.2) WILD-TYPE" "DEL PEAK 33(18Q21.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 33(18Q21.2) MUTATED"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 33(18Q21.2) MUTATED"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 33(18Q21.2) MUTATED" "DEL PEAK 33(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 33(18Q21.2) WILD-TYPE"   "DEL PEAK 33(18Q21.2) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 33(18Q21.2) WILD-TYPE" "DEL PEAK 33(18Q21.2) WILD-TYPE" 
[1] "hr=" "1"  
D56V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 33(18Q21.2) MUTATED          1        1         1         3
  DEL PEAK 33(18Q21.2) WILD-TYPE        1        0         2         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 33(18Q21.2) MUTATED            3          2          1
  DEL PEAK 33(18Q21.2) WILD-TYPE          2          1          0
D56V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 33(18Q21.2) MUTATED    2  2     8
  DEL PEAK 33(18Q21.2) WILD-TYPE  2  5     3
D56V4, multiclass
       clus
vv      DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE
  T1                               2                              2
  T2                               2                              5
  T3+T4                            8                              3
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 33(18Q21.2) MUTATED    4  5     3
  DEL PEAK 33(18Q21.2) WILD-TYPE  4  5     1
D56V5, multiclass
       clus
vv      DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE
  N0                               4                              4
  N1                               5                              5
  N2+N3                            3                              1
D56V6, binary
                                cls
clus                              0  1
  DEL PEAK 33(18Q21.2) MUTATED    0 12
  DEL PEAK 33(18Q21.2) WILD-TYPE  3  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(18Q21.2) MUTATED      0   12
  DEL PEAK 33(18Q21.2) WILD-TYPE    3    7
        clus
vv       DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE
  FEMALE                            0                              3
  MALE                             12                              7
D56V7, continuous

Clustering(57) Variable = DEL PEAK 34(19P13.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 34(19P13.3) MUTATED   9 3
  DEL PEAK 34(19P13.3) WILD-TYPE 3 3
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            12                              6 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                             3                              3 
$`DEL PEAK 34(19P13.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.26         0.53         0.79         3.48         3.68 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX TCGA-LN-A4A2 
        4.08         3.32         1.38        30.71         7.43         0.13 

$`DEL PEAK 34(19P13.3) WILD-TYPE`
TCGA-IG-A625 TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
        0.36        18.35         3.16        29.00         7.10         0.07 

  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                         30.71                          29.00 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                          2.35                           5.13 
[1] "0.0 - 30.7 (2.3)" "0.1 - 29.0 (5.1)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 34(19P13.3) MUTATED"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 34(19P13.3) MUTATED"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 34(19P13.3) WILD-TYPE"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 34(19P13.3) MUTATED"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 34(19P13.3) WILD-TYPE"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "DEL PEAK 34(19P13.3) MUTATED" "DEL PEAK 34(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 34(19P13.3) MUTATED" "DEL PEAK 34(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 34(19P13.3) WILD-TYPE"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 34(19P13.3) MUTATED" "DEL PEAK 34(19P13.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 34(19P13.3) MUTATED"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 34(19P13.3) MUTATED"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 34(19P13.3) WILD-TYPE"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 34(19P13.3) MUTATED"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 34(19P13.3) WILD-TYPE"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "DEL PEAK 34(19P13.3) MUTATED" "DEL PEAK 34(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 34(19P13.3) MUTATED" "DEL PEAK 34(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 34(19P13.3) WILD-TYPE"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 34(19P13.3) MUTATED" "DEL PEAK 34(19P13.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 34(19P13.3) MUTATED"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 34(19P13.3) MUTATED"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 34(19P13.3) WILD-TYPE"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 34(19P13.3) MUTATED"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 34(19P13.3) WILD-TYPE"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
  "DEL PEAK 34(19P13.3) MUTATED" "DEL PEAK 34(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 34(19P13.3) MUTATED" "DEL PEAK 34(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 34(19P13.3) WILD-TYPE"   "DEL PEAK 34(19P13.3) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 34(19P13.3) MUTATED" "DEL PEAK 34(19P13.3) WILD-TYPE" 
[1] "hr=" "1.1"
D57V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 34(19P13.3) MUTATED          1        1         1         5
  DEL PEAK 34(19P13.3) WILD-TYPE        1        0         2         2
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 34(19P13.3) MUTATED            3          2          1
  DEL PEAK 34(19P13.3) WILD-TYPE          2          1          0
D57V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 34(19P13.3) MUTATED    2  5     7
  DEL PEAK 34(19P13.3) WILD-TYPE  2  2     4
D57V4, multiclass
       clus
vv      DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE
  T1                               2                              2
  T2                               5                              2
  T3+T4                            7                              4
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 34(19P13.3) MUTATED    3  8     3
  DEL PEAK 34(19P13.3) WILD-TYPE  5  2     1
D57V5, multiclass
       clus
vv      DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE
  N0                               3                              5
  N1                               8                              2
  N2+N3                            3                              1
D57V6, binary
                                cls
clus                              0  1
  DEL PEAK 34(19P13.3) MUTATED    2 12
  DEL PEAK 34(19P13.3) WILD-TYPE  1  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(19P13.3) MUTATED      2   12
  DEL PEAK 34(19P13.3) WILD-TYPE    1    7
        clus
vv       DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE
  FEMALE                            2                              1
  MALE                             12                              7
D57V7, continuous

Clustering(58) Variable = DEL PEAK 35(19Q13.31) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 35(19Q13.31) MUTATED   4 1
  DEL PEAK 35(19Q13.31) WILD-TYPE 8 5
  DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE 
                              5                              13 
  DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE 
                              1                               5 
$`DEL PEAK 35(19Q13.31) MUTATED`
TCGA-IG-A50L TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OX TCGA-LN-A4A2 
        0.53         4.08        30.71         7.43         0.13 

$`DEL PEAK 35(19Q13.31) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.26         0.79         0.36         3.48         3.68 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         3.32         1.38         3.16        29.00         7.10 
TCGA-LN-A4A9 
        0.07 

  DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE 
                           0.13                            0.03 
  DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE 
                          30.71                           29.00 
  DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE 
                           4.08                            3.16 
[1] "0.1 - 30.7 (4.1)" "0.0 - 29.0 (3.2)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 35(19Q13.31) MUTATED" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 35(19Q13.31) WILD-TYPE"   "DEL PEAK 35(19Q13.31) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
  "DEL PEAK 35(19Q13.31) MUTATED" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 35(19Q13.31) WILD-TYPE"   "DEL PEAK 35(19Q13.31) MUTATED" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "DEL PEAK 35(19Q13.31) MUTATED" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 35(19Q13.31) MUTATED" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 35(19Q13.31) WILD-TYPE"   "DEL PEAK 35(19Q13.31) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
  "DEL PEAK 35(19Q13.31) MUTATED" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 35(19Q13.31) WILD-TYPE"   "DEL PEAK 35(19Q13.31) MUTATED" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "DEL PEAK 35(19Q13.31) MUTATED" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 35(19Q13.31) MUTATED" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 35(19Q13.31) WILD-TYPE"   "DEL PEAK 35(19Q13.31) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 35(19Q13.31) WILD-TYPE" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
  "DEL PEAK 35(19Q13.31) MUTATED" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 35(19Q13.31) WILD-TYPE"   "DEL PEAK 35(19Q13.31) MUTATED" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
  "DEL PEAK 35(19Q13.31) MUTATED" "DEL PEAK 35(19Q13.31) WILD-TYPE" 
[1] "hr=" "2.7"
D58V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 35(19Q13.31) MUTATED          1        0         1         2
  DEL PEAK 35(19Q13.31) WILD-TYPE        1        1         2         5
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 35(19Q13.31) MUTATED            2          0          0
  DEL PEAK 35(19Q13.31) WILD-TYPE          3          3          1
D58V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 35(19Q13.31) MUTATED    1  2     3
  DEL PEAK 35(19Q13.31) WILD-TYPE  3  5     8
D58V4, multiclass
       clus
vv      DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE
  T1                                1                               3
  T2                                2                               5
  T3+T4                             3                               8
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 35(19Q13.31) MUTATED    2  4     0
  DEL PEAK 35(19Q13.31) WILD-TYPE  6  6     4
D58V5, multiclass
       clus
vv      DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE
  N0                                2                               6
  N1                                4                               6
  N2+N3                             0                               4
D58V6, binary
                                 cls
clus                               0  1
  DEL PEAK 35(19Q13.31) MUTATED    2  4
  DEL PEAK 35(19Q13.31) WILD-TYPE  1 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(19Q13.31) MUTATED      2    4
  DEL PEAK 35(19Q13.31) WILD-TYPE    1   15
        clus
vv       DEL PEAK 35(19Q13.31) MUTATED DEL PEAK 35(19Q13.31) WILD-TYPE
  FEMALE                             2                               1
  MALE                               4                              15
D58V7, continuous

Clustering(59) Variable = DEL PEAK 36(20P12.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 36(20P12.1) MUTATED   3 0
  DEL PEAK 36(20P12.1) WILD-TYPE 9 6
  DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE 
                             3                             15 
  DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE 
                             0                              6 
$`DEL PEAK 36(20P12.1) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OO 
        0.26         3.68         3.32 

$`DEL PEAK 36(20P12.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OM 
        0.03         0.53         0.79         0.36         3.48         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         1.38         3.16        30.71        29.00         7.10 
TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.43         0.13         0.07 

  DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE 
                          3.68                          30.71 
  DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE 
                          3.32                           3.16 
[1] "0.3 - 3.7 (3.3)"  "0.0 - 30.7 (3.2)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 36(20P12.1) WILD-TYPE"   "DEL PEAK 36(20P12.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 36(20P12.1) MUTATED" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 36(20P12.1) WILD-TYPE"   "DEL PEAK 36(20P12.1) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 36(20P12.1) WILD-TYPE"   "DEL PEAK 36(20P12.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 36(20P12.1) MUTATED" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 36(20P12.1) WILD-TYPE"   "DEL PEAK 36(20P12.1) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 36(20P12.1) WILD-TYPE"   "DEL PEAK 36(20P12.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 36(20P12.1) MUTATED" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 36(20P12.1) WILD-TYPE"   "DEL PEAK 36(20P12.1) MUTATED" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
[1] "hr="     "2.5e+08"
D59V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 36(20P12.1) MUTATED          0        0         0         1
  DEL PEAK 36(20P12.1) WILD-TYPE        2        1         3         6
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 36(20P12.1) MUTATED            0          1          1
  DEL PEAK 36(20P12.1) WILD-TYPE          5          2          0
D59V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 36(20P12.1) MUTATED    1  0     2
  DEL PEAK 36(20P12.1) WILD-TYPE  3  7     9
D59V4, multiclass
       clus
vv      DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE
  T1                               1                              3
  T2                               0                              7
  T3+T4                            2                              9
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 36(20P12.1) MUTATED    0  1     2
  DEL PEAK 36(20P12.1) WILD-TYPE  8  9     2
D59V5, multiclass
       clus
vv      DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE
  N0                               0                              8
  N1                               1                              9
  N2+N3                            2                              2
D59V6, binary
                                cls
clus                              0  1
  DEL PEAK 36(20P12.1) MUTATED    0  3
  DEL PEAK 36(20P12.1) WILD-TYPE  3 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(20P12.1) MUTATED      0    3
  DEL PEAK 36(20P12.1) WILD-TYPE    3   16
        clus
vv       DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE
  FEMALE                            0                              3
  MALE                              3                             16
D59V7, continuous
[1] "Remove cluster labels:"       "DEL PEAK 36(20P12.1) MUTATED"
clus
  DEL PEAK 36(20P12.1) MUTATED DEL PEAK 36(20P12.1) WILD-TYPE 
                             1                             13 
                    TCGA-IG-A3Y9                     TCGA-IG-A3YA 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A50L 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-IG-A5B8                     TCGA-L5-A4OE 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OU 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 36(20P12.1) WILD-TYPE" "DEL PEAK 36(20P12.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 36(20P12.1) WILD-TYPE" 

Clustering(60) Variable = DEL PEAK 37(21Q21.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 37(21Q21.1) MUTATED   8 5
  DEL PEAK 37(21Q21.1) WILD-TYPE 4 1
  DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE 
                            13                              5 
  DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE 
                             5                              1 
$`DEL PEAK 37(21Q21.1) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.03         0.26         0.53         0.79         3.48         3.68 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        4.08        18.35         3.16        30.71        29.00         7.10 
TCGA-L5-A4OX 
        7.43 

$`DEL PEAK 37(21Q21.1) WILD-TYPE`
TCGA-IG-A625 TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.36         3.32         1.38         0.13         0.07 

  DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE 
                         30.71                           3.32 
  DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE 
                          3.68                           0.36 
[1] "0.0 - 30.7 (3.7)" "0.1 - 3.3 (0.4)" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 37(21Q21.1) WILD-TYPE"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK 37(21Q21.1) MUTATED" "DEL PEAK 37(21Q21.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 37(21Q21.1) WILD-TYPE"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 37(21Q21.1) WILD-TYPE" "DEL PEAK 37(21Q21.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 37(21Q21.1) WILD-TYPE"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK 37(21Q21.1) MUTATED" "DEL PEAK 37(21Q21.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 37(21Q21.1) WILD-TYPE"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 37(21Q21.1) WILD-TYPE" "DEL PEAK 37(21Q21.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 37(21Q21.1) WILD-TYPE"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK 37(21Q21.1) MUTATED" "DEL PEAK 37(21Q21.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 37(21Q21.1) WILD-TYPE"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 37(21Q21.1) MUTATED"   "DEL PEAK 37(21Q21.1) MUTATED" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 37(21Q21.1) WILD-TYPE" "DEL PEAK 37(21Q21.1) WILD-TYPE" 
[1] "hr=" "2.9"
D60V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 37(21Q21.1) MUTATED          2        1         1         6
  DEL PEAK 37(21Q21.1) WILD-TYPE        0        0         2         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 37(21Q21.1) MUTATED            3          2          0
  DEL PEAK 37(21Q21.1) WILD-TYPE          2          1          1
D60V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 37(21Q21.1) MUTATED    4  4     7
  DEL PEAK 37(21Q21.1) WILD-TYPE  0  3     4
D60V4, multiclass
       clus
vv      DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE
  T1                               4                              0
  T2                               4                              3
  T3+T4                            7                              4
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 37(21Q21.1) MUTATED    6  7     2
  DEL PEAK 37(21Q21.1) WILD-TYPE  2  3     2
D60V5, multiclass
       clus
vv      DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE
  N0                               6                              2
  N1                               7                              3
  N2+N3                            2                              2
D60V6, binary
                                cls
clus                              0  1
  DEL PEAK 37(21Q21.1) MUTATED    3 12
  DEL PEAK 37(21Q21.1) WILD-TYPE  0  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(21Q21.1) MUTATED      3   12
  DEL PEAK 37(21Q21.1) WILD-TYPE    0    7
        clus
vv       DEL PEAK 37(21Q21.1) MUTATED DEL PEAK 37(21Q21.1) WILD-TYPE
  FEMALE                            3                              0
  MALE                             12                              7
D60V7, continuous

Clustering(61) Variable = DEL PEAK 38(21Q22.12) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 38(21Q22.12) MUTATED   7 4
  DEL PEAK 38(21Q22.12) WILD-TYPE 5 2
  DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE 
                             11                               7 
  DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE 
                              4                               2 
$`DEL PEAK 38(21Q22.12) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4OM 
        0.03         0.26         0.53         0.79         3.48         4.08 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.71        29.00         7.10         7.43 

$`DEL PEAK 38(21Q22.12) WILD-TYPE`
TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-LN-A4A2 
        0.36         3.68        18.35         3.32         1.38         0.13 
TCGA-LN-A4A9 
        0.07 

  DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE 
                           0.03                            0.07 
  DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE 
                          30.71                           18.35 
  DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE 
                           3.48                            1.38 
[1] "0.0 - 30.7 (3.5)" "0.1 - 18.4 (1.4)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 38(21Q22.12) WILD-TYPE"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 38(21Q22.12) WILD-TYPE"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 38(21Q22.12) WILD-TYPE" "DEL PEAK 38(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 38(21Q22.12) WILD-TYPE"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
"DEL PEAK 38(21Q22.12) WILD-TYPE" "DEL PEAK 38(21Q22.12) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 38(21Q22.12) WILD-TYPE"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 38(21Q22.12) WILD-TYPE"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 38(21Q22.12) WILD-TYPE" "DEL PEAK 38(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 38(21Q22.12) WILD-TYPE"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
"DEL PEAK 38(21Q22.12) WILD-TYPE" "DEL PEAK 38(21Q22.12) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-IG-A50L                      TCGA-IG-A5B8 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-IG-A625                      TCGA-L5-A4OE 
"DEL PEAK 38(21Q22.12) WILD-TYPE"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4OF                      TCGA-L5-A4OM 
"DEL PEAK 38(21Q22.12) WILD-TYPE"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 38(21Q22.12) WILD-TYPE" "DEL PEAK 38(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OR 
"DEL PEAK 38(21Q22.12) WILD-TYPE"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4OS                      TCGA-L5-A4OU 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
  "DEL PEAK 38(21Q22.12) MUTATED"   "DEL PEAK 38(21Q22.12) MUTATED" 
                     TCGA-LN-A4A2                      TCGA-LN-A4A9 
"DEL PEAK 38(21Q22.12) WILD-TYPE" "DEL PEAK 38(21Q22.12) WILD-TYPE" 
[1] "hr=" "1.2"
D61V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 38(21Q22.12) MUTATED          2        1         1         4
  DEL PEAK 38(21Q22.12) WILD-TYPE        0        0         2         3
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 38(21Q22.12) MUTATED            3          2          0
  DEL PEAK 38(21Q22.12) WILD-TYPE          2          1          1
D61V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 38(21Q22.12) MUTATED    2  4     7
  DEL PEAK 38(21Q22.12) WILD-TYPE  2  3     4
D61V4, multiclass
       clus
vv      DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE
  T1                                2                               2
  T2                                4                               3
  T3+T4                             7                               4
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 38(21Q22.12) MUTATED    6  5     2
  DEL PEAK 38(21Q22.12) WILD-TYPE  2  5     2
D61V5, multiclass
       clus
vv      DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE
  N0                                6                               2
  N1                                5                               5
  N2+N3                             2                               2
D61V6, binary
                                 cls
clus                               0  1
  DEL PEAK 38(21Q22.12) MUTATED    3 10
  DEL PEAK 38(21Q22.12) WILD-TYPE  0  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(21Q22.12) MUTATED      3   10
  DEL PEAK 38(21Q22.12) WILD-TYPE    0    9
        clus
vv       DEL PEAK 38(21Q22.12) MUTATED DEL PEAK 38(21Q22.12) WILD-TYPE
  FEMALE                             3                               0
  MALE                              10                               9
D61V7, continuous

Clustering(62) Variable = DEL PEAK 39(22Q11.1) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 39(22Q11.1) MUTATED   6 4
  DEL PEAK 39(22Q11.1) WILD-TYPE 6 2
  DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE 
                            10                              8 
  DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE 
                             4                              2 
$`DEL PEAK 39(22Q11.1) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A4OE TCGA-L5-A4ON 
        0.03         0.26         0.53         0.79         3.48        18.35 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        3.16        30.71        29.00         7.10 

$`DEL PEAK 39(22Q11.1) WILD-TYPE`
TCGA-IG-A625 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX 
        0.36         3.68         4.08         3.32         1.38         7.43 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE 
                         30.71                           7.43 
  DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE 
                          3.32                           2.35 
[1] "0.0 - 30.7 (3.3)" "0.1 - 7.4 (2.3)" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 39(22Q11.1) MUTATED"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 39(22Q11.1) MUTATED"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 39(22Q11.1) WILD-TYPE"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 39(22Q11.1) WILD-TYPE" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK 39(22Q11.1) MUTATED" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 39(22Q11.1) WILD-TYPE"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 39(22Q11.1) MUTATED"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 39(22Q11.1) MUTATED" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 39(22Q11.1) WILD-TYPE" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 39(22Q11.1) MUTATED"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 39(22Q11.1) MUTATED"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 39(22Q11.1) WILD-TYPE"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 39(22Q11.1) WILD-TYPE" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK 39(22Q11.1) MUTATED" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 39(22Q11.1) WILD-TYPE"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 39(22Q11.1) MUTATED"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 39(22Q11.1) MUTATED" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 39(22Q11.1) WILD-TYPE" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 39(22Q11.1) MUTATED"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
  "DEL PEAK 39(22Q11.1) MUTATED"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 39(22Q11.1) WILD-TYPE"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 39(22Q11.1) WILD-TYPE" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
  "DEL PEAK 39(22Q11.1) MUTATED" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 39(22Q11.1) WILD-TYPE"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
  "DEL PEAK 39(22Q11.1) MUTATED"   "DEL PEAK 39(22Q11.1) MUTATED" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
  "DEL PEAK 39(22Q11.1) MUTATED" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
"DEL PEAK 39(22Q11.1) WILD-TYPE" "DEL PEAK 39(22Q11.1) WILD-TYPE" 
[1] "hr=" "1.3"
D62V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 39(22Q11.1) MUTATED          1        1         1         4
  DEL PEAK 39(22Q11.1) WILD-TYPE        1        0         2         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 39(22Q11.1) MUTATED            2          2          0
  DEL PEAK 39(22Q11.1) WILD-TYPE          3          1          1
D62V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 39(22Q11.1) MUTATED    2  3     6
  DEL PEAK 39(22Q11.1) WILD-TYPE  2  4     5
D62V4, multiclass
       clus
vv      DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE
  T1                               2                              2
  T2                               3                              4
  T3+T4                            6                              5
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 39(22Q11.1) MUTATED    3  6     2
  DEL PEAK 39(22Q11.1) WILD-TYPE  5  4     2
D62V5, multiclass
       clus
vv      DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE
  N0                               3                              5
  N1                               6                              4
  N2+N3                            2                              2
D62V6, binary
                                cls
clus                              0  1
  DEL PEAK 39(22Q11.1) MUTATED    2  9
  DEL PEAK 39(22Q11.1) WILD-TYPE  1 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q11.1) MUTATED      2    9
  DEL PEAK 39(22Q11.1) WILD-TYPE    1   10
        clus
vv       DEL PEAK 39(22Q11.1) MUTATED DEL PEAK 39(22Q11.1) WILD-TYPE
  FEMALE                            2                              1
  MALE                              9                             10
D62V7, continuous

Clustering(63) Variable = DEL PEAK 40(XP21.1) MUTATION ANALYSIS
D63V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 40(XP21.1) MUTATED   7 2
  DEL PEAK 40(XP21.1) WILD-TYPE 5 4
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                            9                             9 
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                            2                             4 
$`DEL PEAK 40(XP21.1) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM 
        0.26         0.53         0.36         3.48         3.68         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-LN-A4A2 
       18.35         1.38         0.13 

$`DEL PEAK 40(XP21.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        0.03         0.79         3.32         3.16        30.71        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        7.10         7.43         0.07 

  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                        18.35                         30.71 
  DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE 
                         1.38                          3.32 
[1] "0.1 - 18.4 (1.4)" "0.0 - 30.7 (3.3)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 40(XP21.1) WILD-TYPE"   "DEL PEAK 40(XP21.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 40(XP21.1) MUTATED"   "DEL PEAK 40(XP21.1) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 40(XP21.1) MUTATED"   "DEL PEAK 40(XP21.1) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 40(XP21.1) WILD-TYPE" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 40(XP21.1) WILD-TYPE" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 40(XP21.1) WILD-TYPE"   "DEL PEAK 40(XP21.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 40(XP21.1) MUTATED"   "DEL PEAK 40(XP21.1) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 40(XP21.1) MUTATED"   "DEL PEAK 40(XP21.1) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 40(XP21.1) WILD-TYPE" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 40(XP21.1) WILD-TYPE" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 40(XP21.1) WILD-TYPE"   "DEL PEAK 40(XP21.1) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 40(XP21.1) MUTATED"   "DEL PEAK 40(XP21.1) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 40(XP21.1) MUTATED"   "DEL PEAK 40(XP21.1) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 40(XP21.1) WILD-TYPE" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 40(XP21.1) WILD-TYPE" "DEL PEAK 40(XP21.1) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 40(XP21.1) MUTATED" "DEL PEAK 40(XP21.1) WILD-TYPE" 
[1] "hr=" "1"  
D63V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 40(XP21.1) MUTATED          1        0         1         3
  DEL PEAK 40(XP21.1) WILD-TYPE        1        1         2         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 40(XP21.1) MUTATED            4          3          0
  DEL PEAK 40(XP21.1) WILD-TYPE          1          0          1
D63V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 40(XP21.1) MUTATED    3  2     7
  DEL PEAK 40(XP21.1) WILD-TYPE  1  5     4
D63V4, multiclass
       clus
vv      DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE
  T1                              3                             1
  T2                              2                             5
  T3+T4                           7                             4
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 40(XP21.1) MUTATED    4  5     3
  DEL PEAK 40(XP21.1) WILD-TYPE  4  5     1
D63V5, multiclass
       clus
vv      DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE
  N0                              4                             4
  N1                              5                             5
  N2+N3                           3                             1
D63V6, binary
                               cls
clus                             0  1
  DEL PEAK 40(XP21.1) MUTATED    1 11
  DEL PEAK 40(XP21.1) WILD-TYPE  2  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 40(XP21.1) MUTATED      1   11
  DEL PEAK 40(XP21.1) WILD-TYPE    2    8
        clus
vv       DEL PEAK 40(XP21.1) MUTATED DEL PEAK 40(XP21.1) WILD-TYPE
  FEMALE                           1                             2
  MALE                            11                             8
D63V7, continuous

Clustering(64) Variable = DEL PEAK 41(XP11.3) MUTATION ANALYSIS
D64V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 41(XP11.3) MUTATED   8 2
  DEL PEAK 41(XP11.3) WILD-TYPE 4 4
  DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE 
                           10                             8 
  DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE 
                            2                             4 
$`DEL PEAK 41(XP11.3) MUTATED`
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE TCGA-L5-A4OF 
        0.26         0.53         0.79         0.36         3.48         3.68 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-LN-A4A2 TCGA-LN-A4A9 
        4.08        18.35         0.13         0.07 

$`DEL PEAK 41(XP11.3) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        0.03         3.32         1.38         3.16        30.71        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX 
        7.10         7.43 

  DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE 
                        18.35                         30.71 
  DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE 
                         0.66                          5.21 
[1] "0.1 - 18.4 (0.7)" "0.0 - 30.7 (5.2)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 41(XP11.3) WILD-TYPE"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 41(XP11.3) MUTATED" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 41(XP11.3) WILD-TYPE" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 41(XP11.3) WILD-TYPE" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 41(XP11.3) WILD-TYPE" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 41(XP11.3) WILD-TYPE"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 41(XP11.3) MUTATED" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 41(XP11.3) WILD-TYPE" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 41(XP11.3) WILD-TYPE" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 41(XP11.3) WILD-TYPE" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 41(XP11.3) WILD-TYPE"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-IG-A50L                    TCGA-IG-A5B8 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-IG-A625                    TCGA-L5-A4OE 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-L5-A4OF                    TCGA-L5-A4OM 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
                   TCGA-L5-A4ON                    TCGA-L5-A4OO 
  "DEL PEAK 41(XP11.3) MUTATED" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OQ                    TCGA-L5-A4OR 
"DEL PEAK 41(XP11.3) WILD-TYPE" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OS                    TCGA-L5-A4OU 
"DEL PEAK 41(XP11.3) WILD-TYPE" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OW                    TCGA-L5-A4OX 
"DEL PEAK 41(XP11.3) WILD-TYPE" "DEL PEAK 41(XP11.3) WILD-TYPE" 
                   TCGA-LN-A4A2                    TCGA-LN-A4A9 
  "DEL PEAK 41(XP11.3) MUTATED"   "DEL PEAK 41(XP11.3) MUTATED" 
[1] "hr=" "1"  
D64V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 41(XP11.3) MUTATED          1        1         2         3
  DEL PEAK 41(XP11.3) WILD-TYPE        1        0         1         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 41(XP11.3) MUTATED            3          3          0
  DEL PEAK 41(XP11.3) WILD-TYPE          2          0          1
D64V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 41(XP11.3) MUTATED    3  2     8
  DEL PEAK 41(XP11.3) WILD-TYPE  1  5     3
D64V4, multiclass
       clus
vv      DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE
  T1                              3                             1
  T2                              2                             5
  T3+T4                           8                             3
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 41(XP11.3) MUTATED    6  4     3
  DEL PEAK 41(XP11.3) WILD-TYPE  2  6     1
D64V5, multiclass
       clus
vv      DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE
  N0                              6                             2
  N1                              4                             6
  N2+N3                           3                             1
D64V6, binary
                               cls
clus                             0  1
  DEL PEAK 41(XP11.3) MUTATED    1 12
  DEL PEAK 41(XP11.3) WILD-TYPE  2  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 41(XP11.3) MUTATED      1   12
  DEL PEAK 41(XP11.3) WILD-TYPE    2    7
        clus
vv       DEL PEAK 41(XP11.3) MUTATED DEL PEAK 41(XP11.3) WILD-TYPE
  FEMALE                           1                             2
  MALE                            12                             7
D64V7, continuous

Clustering(65) Variable = DEL PEAK 42(XQ21.33) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 42(XQ21.33) MUTATED   3 1
  DEL PEAK 42(XQ21.33) WILD-TYPE 9 5
  DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE 
                             4                             14 
  DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE 
                             1                              5 
$`DEL PEAK 42(XQ21.33) MUTATED`
TCGA-L5-A4OM TCGA-L5-A4OR TCGA-LN-A4A2 TCGA-LN-A4A9 
        4.08         3.16         0.13         0.07 

$`DEL PEAK 42(XQ21.33) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OE 
        0.03         0.26         0.53         0.79         0.36         3.48 
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        3.68        18.35         3.32         1.38        30.71        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX 
        7.10         7.43 

  DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE 
                          4.08                          30.71 
  DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE 
                         1.645                          3.400 
[1] "0.1 - 4.1 (1.6)"  "0.0 - 30.7 (3.4)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 42(XQ21.33) WILD-TYPE"   "DEL PEAK 42(XQ21.33) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 42(XQ21.33) WILD-TYPE"   "DEL PEAK 42(XQ21.33) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 42(XQ21.33) MUTATED"   "DEL PEAK 42(XQ21.33) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 42(XQ21.33) WILD-TYPE"   "DEL PEAK 42(XQ21.33) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 42(XQ21.33) WILD-TYPE"   "DEL PEAK 42(XQ21.33) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 42(XQ21.33) MUTATED"   "DEL PEAK 42(XQ21.33) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-IG-A50L                     TCGA-IG-A5B8 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-IG-A625                     TCGA-L5-A4OE 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OF                     TCGA-L5-A4OM 
"DEL PEAK 42(XQ21.33) WILD-TYPE"   "DEL PEAK 42(XQ21.33) MUTATED" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OR 
"DEL PEAK 42(XQ21.33) WILD-TYPE"   "DEL PEAK 42(XQ21.33) MUTATED" 
                    TCGA-L5-A4OS                     TCGA-L5-A4OU 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A9 
  "DEL PEAK 42(XQ21.33) MUTATED"   "DEL PEAK 42(XQ21.33) MUTATED" 
[1] "hr=" "2.2"
D65V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 42(XQ21.33) MUTATED          2        0         2         0
  DEL PEAK 42(XQ21.33) WILD-TYPE        0        1         1         7
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 42(XQ21.33) MUTATED            0          0          0
  DEL PEAK 42(XQ21.33) WILD-TYPE          5          3          1
D65V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 42(XQ21.33) MUTATED    2  1     1
  DEL PEAK 42(XQ21.33) WILD-TYPE  2  6    10
D65V4, multiclass
       clus
vv      DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE
  T1                               2                              2
  T2                               1                              6
  T3+T4                            1                             10
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 42(XQ21.33) MUTATED    4  0     0
  DEL PEAK 42(XQ21.33) WILD-TYPE  4 10     4
D65V5, multiclass
       clus
vv      DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE
  N0                               4                              4
  N1                               0                             10
  N2+N3                            0                              4
D65V6, binary
                                cls
clus                              0  1
  DEL PEAK 42(XQ21.33) MUTATED    1  3
  DEL PEAK 42(XQ21.33) WILD-TYPE  2 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(XQ21.33) MUTATED      1    3
  DEL PEAK 42(XQ21.33) WILD-TYPE    2   16
        clus
vv       DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE
  FEMALE                            1                              2
  MALE                              3                             16
D65V7, continuous
[1] "Remove cluster labels:"       "DEL PEAK 42(XQ21.33) MUTATED"
clus
  DEL PEAK 42(XQ21.33) MUTATED DEL PEAK 42(XQ21.33) WILD-TYPE 
                             2                             12 
                    TCGA-IG-A3Y9                     TCGA-IG-A3YA 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A50L 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-IG-A5B8                     TCGA-L5-A4OE 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OU 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 42(XQ21.33) WILD-TYPE" "DEL PEAK 42(XQ21.33) WILD-TYPE" 
> q(save="no")
