
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/4427012/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/ESCA-TP/4396310/ESCA-TP.clin.merged.picked.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/GDAC_clinicalDataPicker/ESCA-TP/4396310/ESCA-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/4427012/transformed.cor.cli.txt"

nPatients in clinical file=19, in cluster file=63, common to both=19
[1] "Reduce the number of clustering variables from 65 to 63."
[1] 63 19
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            7                            12 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            7                            12 
[1] "AMP PEAK  2(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE 
                           11                             8 
  AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE 
                           11                             8 
[1] "AMP PEAK  3(2Q14.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                            6                            13 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                            6                            13 
[1] "AMP PEAK  4(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           16                             3 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           16                             3 
[1] "AMP PEAK  5(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                             7                             12 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                             7                             12 
[1] "AMP PEAK  6(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                            8                            11 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                            8                            11 
[1] "AMP PEAK  7(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          6                          13 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          6                          13 
[1] "AMP PEAK  8(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                           14                             5 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                           14                             5 
[1] "AMP PEAK  9(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                           14                             5 
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                           14                             5 
[1] "AMP PEAK 10(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                            12                              7 
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                            12                              7 
[1] "AMP PEAK 11(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            16                              3 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            16                              3 
[1] "AMP PEAK 13(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                           4                           15 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                           4                           15 
[1] "AMP PEAK 14(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            11                              8 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            11                              8 
[1] "AMP PEAK 15(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE 
                              8                              11 
  AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE 
                              8                              11 
[1] "AMP PEAK 16(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                             8                             11 
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                             8                             11 
[1] "AMP PEAK 17(14Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE 
                             6                             13 
  AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE 
                             6                             13 
[1] "AMP PEAK 18(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                           9                           10 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                           9                           10 
[1] "AMP PEAK 19(17Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                             9                             10 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                             9                             10 
[1] "AMP PEAK 20(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE 
                              5                              14 
  AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE 
                              5                              14 
[1] "AMP PEAK 21(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE 
                             5                             14 
  AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE 
                             5                             14 
[1] "AMP PEAK 22(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                             3                             16 
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                             3                             16 
[1] "AMP PEAK 23(19P13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE 
                              4                              15 
  AMP PEAK 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE 
                              4                              15 
[1] "AMP PEAK 24(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                           8                           11 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                           8                           11 
[1] "AMP PEAK 25(XP11.4) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                            4                            15 
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                            4                            15 
[1] "DEL PEAK  1(1P36.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                             8                             11 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                             8                             11 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            8                            11 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            8                            11 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          3                          16 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          3                          16 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            7                            12 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            7                            12 
[1] "DEL PEAK  5(2Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE 
                          6                          13 
  DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE 
                          6                          13 
[1] "DEL PEAK  6(3P26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                           11                             8 
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                           11                             8 
[1] "DEL PEAK  7(3P14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           13                             6 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           13                             6 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           14                             5 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           14                             5 
[1] "DEL PEAK 10(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             3                             16 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             3                             16 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           11                             8 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           11                             8 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                            9                            10 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                            9                            10 
[1] "DEL PEAK 13(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           12                             7 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           12                             7 
[1] "DEL PEAK 14(5Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                           12                             7 
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                           12                             7 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                            8                            11 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                            8                            11 
[1] "DEL PEAK 16(6Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE 
                            3                            16 
  DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE 
                            3                            16 
[1] "DEL PEAK 17(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            8                            11 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            8                            11 
[1] "DEL PEAK 18(7Q36.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                            9                            10 
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                            9                            10 
[1] "DEL PEAK 19(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                           10                             9 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                           10                             9 
[1] "DEL PEAK 20(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                           15                             4 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                           15                             4 
[1] "DEL PEAK 21(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                              4                              15 
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                              4                              15 
[1] "DEL PEAK 22(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              8                              11 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              8                              11 
[1] "DEL PEAK 23(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                             5                             14 
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                             5                             14 
[1] "DEL PEAK 24(11Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                             9                             10 
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                             9                             10 
[1] "DEL PEAK 25(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                           5                           14 
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                           5                           14 
[1] "DEL PEAK 26(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                             11                               8 
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                             11                               8 
[1] "DEL PEAK 27(15Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                             4                             15 
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                             4                             15 
[1] "DEL PEAK 28(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                             9                             10 
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                             9                             10 
[1] "DEL PEAK 29(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                             3                             16 
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                             3                             16 
[1] "DEL PEAK 30(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE 
                             9                             10 
  DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE 
                             9                             10 
[1] "DEL PEAK 31(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE 
                            10                              9 
  DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE 
                            10                              9 
[1] "DEL PEAK 32(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            12                              7 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            12                              7 
[1] "DEL PEAK 33(19Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE 
                              4                              15 
  DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE 
                              4                              15 
[1] "DEL PEAK 34(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                             3                             16 
  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                             3                             16 
[1] "DEL PEAK 35(21Q22.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE 
                             11                               8 
  DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE 
                             11                               8 
[1] "DEL PEAK 36(22Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE 
                             9                             10 
  DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE 
                             9                             10 
[1] "DEL PEAK 37(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE 
                            7                            12 
  DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE 
                            7                            12 
[1] "DEL PEAK 38(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                           10                             9 
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                           10                             9 
[1] "DEL PEAK 39(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE 
                           10                             9 
  DEL PEAK 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE 
                           10                             9 
[1] "DEL PEAK 40(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE 
                             4                             15 
  DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE 
                             4                             15 
[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" "BATCHNUMBER"          

Input Data has 12 rows and 19 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D 
          NA           NA           NA            1            8           NA 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
         106          112          124           NA          101           NA 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
          NA          934          882           NA           NA            4 
TCGA-LN-A4A9 
           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=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	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=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=3,	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 19 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, 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  6  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    4     7     8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 4  7  6  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    4     7     8 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
 7  9  2  1 
[1] "table(vv)"
vv
      N0 N1+N2+N3 
       7       12 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
 7  9  2  1 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 7

$Class1_nSamples
[1] 12

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2+N3"


      N0 N1+N2+N3 
       7       12 
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=10, 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 8 2
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            5                            10 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            3                             2 
$`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-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         0.26         3.48         3.68         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 
       30.71        29.00         7.43         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                          3.40 
[1] "0.1 - 18.4 (4.1)" "0.0 - 30.7 (3.4)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  1(1P34.2) MUTATED"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  1(1P34.2) MUTATED"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  1(1P34.2) MUTATED"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  1(1P34.2) WILD-TYPE"   "AMP PEAK  1(1P34.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  1(1P34.2) WILD-TYPE" "AMP PEAK  1(1P34.2) WILD-TYPE" 
                   TCGA-LN-A4A9 
  "AMP PEAK  1(1P34.2) MUTATED" 
[1] "hr=" "3.1"
D1V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  1(1P34.2) MUTATED          1         1         3          2
  AMP PEAK  1(1P34.2) WILD-TYPE        1         2         4          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  AMP PEAK  1(1P34.2) MUTATED            0          0
  AMP PEAK  1(1P34.2) WILD-TYPE          2          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     7
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                             7
                               vv
clus                            N0 N1+N2+N3
  AMP PEAK  1(1P34.2) MUTATED    3        4
  AMP PEAK  1(1P34.2) WILD-TYPE  4        8
D1V5, multiclass
          clus
vv         AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                                 3                             4
  N1+N2+N3                           4                             8
D1V6, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED    2  5
  AMP PEAK  1(1P34.2) WILD-TYPE  1 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      2    5
  AMP PEAK  1(1P34.2) WILD-TYPE    1   11
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                           2                             1
  MALE                             5                            11
D1V7, continuous

Clustering(2) Variable = AMP PEAK  2(1Q42.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  2(1Q42.3) MUTATED   5 3
  AMP PEAK  2(1Q42.3) WILD-TYPE 5 2
  AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE 
                            8                             7 
  AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE 
                            3                             2 
$`AMP PEAK  2(1Q42.3) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OX 
        0.03         3.68         4.08        18.35         1.38         7.43 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

$`AMP PEAK  2(1Q42.3) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        0.26         3.48         3.32         3.16        30.71        29.00 
TCGA-L5-A4OW 
        7.10 

  AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE 
                         0.03                          0.26 
  AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE 
                        18.35                         30.71 
  AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE 
                         2.53                          3.48 
[1] "0.0 - 18.4 (2.5)" "0.3 - 30.7 (3.5)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  2(1Q42.3) MUTATED" "AMP PEAK  2(1Q42.3) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  2(1Q42.3) WILD-TYPE"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  2(1Q42.3) MUTATED"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK  2(1Q42.3) WILD-TYPE"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  2(1Q42.3) WILD-TYPE" "AMP PEAK  2(1Q42.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  2(1Q42.3) WILD-TYPE" "AMP PEAK  2(1Q42.3) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "AMP PEAK  2(1Q42.3) MUTATED"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-LN-A4A9 
  "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  2(1Q42.3) MUTATED" "AMP PEAK  2(1Q42.3) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  2(1Q42.3) WILD-TYPE"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  2(1Q42.3) MUTATED"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK  2(1Q42.3) WILD-TYPE"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  2(1Q42.3) WILD-TYPE" "AMP PEAK  2(1Q42.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  2(1Q42.3) WILD-TYPE" "AMP PEAK  2(1Q42.3) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "AMP PEAK  2(1Q42.3) MUTATED"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-LN-A4A9 
  "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "AMP PEAK  2(1Q42.3) MUTATED" "AMP PEAK  2(1Q42.3) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  2(1Q42.3) WILD-TYPE"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  2(1Q42.3) MUTATED"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK  2(1Q42.3) WILD-TYPE"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  2(1Q42.3) WILD-TYPE" "AMP PEAK  2(1Q42.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  2(1Q42.3) WILD-TYPE" "AMP PEAK  2(1Q42.3) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "AMP PEAK  2(1Q42.3) MUTATED"   "AMP PEAK  2(1Q42.3) MUTATED" 
                   TCGA-LN-A4A9 
  "AMP PEAK  2(1Q42.3) MUTATED" 
[1] "hr=" "2.1"
D2V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  2(1Q42.3) MUTATED          1         2         5          3
  AMP PEAK  2(1Q42.3) WILD-TYPE        1         1         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC
  AMP PEAK  2(1Q42.3) MUTATED            0          0
  AMP PEAK  2(1Q42.3) WILD-TYPE          2          1
D2V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  2(1Q42.3) MUTATED    3  5     3
  AMP PEAK  2(1Q42.3) WILD-TYPE  1  2     5
D2V4, multiclass
       clus
vv      AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE
  T1                              3                             1
  T2                              5                             2
  T3+T4                           3                             5
                               vv
clus                            N0 N1+N2+N3
  AMP PEAK  2(1Q42.3) MUTATED    4        7
  AMP PEAK  2(1Q42.3) WILD-TYPE  3        5
D2V5, multiclass
          clus
vv         AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE
  N0                                 4                             3
  N1+N2+N3                           7                             5
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q42.3) MUTATED    1 10
  AMP PEAK  2(1Q42.3) WILD-TYPE  2  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q42.3) MUTATED      1   10
  AMP PEAK  2(1Q42.3) WILD-TYPE    2    6
        clus
vv       AMP PEAK  2(1Q42.3) MUTATED AMP PEAK  2(1Q42.3) WILD-TYPE
  FEMALE                           1                             2
  MALE                            10                             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 7 3
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                            5                            10 
  AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE 
                            2                             3 
$`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-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OR 
        0.03         0.26         3.48         3.68        18.35         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
       30.71        29.00         7.10         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                          3.58 
[1] "0.1 - 7.4 (3.3)"  "0.0 - 30.7 (3.6)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  3(2Q14.2) MUTATED" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "AMP PEAK  3(2Q14.2) MUTATED"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "AMP PEAK  3(2Q14.2) MUTATED"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  3(2Q14.2) MUTATED" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "AMP PEAK  3(2Q14.2) MUTATED"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "AMP PEAK  3(2Q14.2) MUTATED"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  3(2Q14.2) MUTATED" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "AMP PEAK  3(2Q14.2) MUTATED"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  3(2Q14.2) WILD-TYPE" "AMP PEAK  3(2Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "AMP PEAK  3(2Q14.2) MUTATED"   "AMP PEAK  3(2Q14.2) MUTATED" 
                   TCGA-LN-A4A9 
"AMP PEAK  3(2Q14.2) WILD-TYPE" 
[1] "hr=" "2.6"
D3V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  3(2Q14.2) MUTATED          1         1         1          2
  AMP PEAK  3(2Q14.2) WILD-TYPE        1         2         6          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  AMP PEAK  3(2Q14.2) MUTATED            0          1
  AMP PEAK  3(2Q14.2) WILD-TYPE          2          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     5
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                             5
                               vv
clus                            N0 N1+N2+N3
  AMP PEAK  3(2Q14.2) MUTATED    2        4
  AMP PEAK  3(2Q14.2) WILD-TYPE  5        8
D3V5, multiclass
          clus
vv         AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  N0                                 2                             5
  N1+N2+N3                           4                             8
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(2Q14.2) MUTATED    1  5
  AMP PEAK  3(2Q14.2) WILD-TYPE  2 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q14.2) MUTATED      1    5
  AMP PEAK  3(2Q14.2) WILD-TYPE    2   11
        clus
vv       AMP PEAK  3(2Q14.2) MUTATED AMP PEAK  3(2Q14.2) WILD-TYPE
  FEMALE                           1                             2
  MALE                             5                            11
D3V7, continuous

Clustering(4) Variable = AMP PEAK  4(3Q26.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  4(3Q26.2) MUTATED   8 4
  AMP PEAK  4(3Q26.2) WILD-TYPE 2 1
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                           12                             3 
  AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE 
                            4                             1 
$`AMP PEAK  4(3Q26.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.48         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 

$`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 
                         3.24                          7.43 
[1] "0.0 - 29.0 (3.2)" "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-L5-A4OE                    TCGA-L5-A4OF 
  "AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) WILD-TYPE" 
                   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-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  4(3Q26.2) WILD-TYPE"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
  "AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) WILD-TYPE" 
                   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-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  4(3Q26.2) WILD-TYPE"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
  "AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) WILD-TYPE" 
                   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-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "AMP PEAK  4(3Q26.2) MUTATED"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  4(3Q26.2) WILD-TYPE"   "AMP PEAK  4(3Q26.2) MUTATED" 
                   TCGA-LN-A4A9 
  "AMP PEAK  4(3Q26.2) MUTATED" 
[1] "hr=" "2.3"
D4V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  4(3Q26.2) MUTATED          2         3         4          4
  AMP PEAK  4(3Q26.2) WILD-TYPE        0         0         3          0
                               vv
clus                            STAGE IIIB STAGE IIIC
  AMP PEAK  4(3Q26.2) MUTATED            2          1
  AMP PEAK  4(3Q26.2) WILD-TYPE          0          0
D4V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  4(3Q26.2) MUTATED    3  5     8
  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                           8                             0
                               vv
clus                            N0 N1+N2+N3
  AMP PEAK  4(3Q26.2) MUTATED    7        9
  AMP PEAK  4(3Q26.2) WILD-TYPE  0        3
D4V5, multiclass
          clus
vv         AMP PEAK  4(3Q26.2) MUTATED AMP PEAK  4(3Q26.2) WILD-TYPE
  N0                                 7                             0
  N1+N2+N3                           9                             3
D4V6, binary
                               cls
clus                             0  1
  AMP PEAK  4(3Q26.2) MUTATED    2 14
  AMP PEAK  4(3Q26.2) WILD-TYPE  1  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3Q26.2) MUTATED      2   14
  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                            14                             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 
                           11                             1 
                 TCGA-IG-A3Y9                  TCGA-IG-A3YA 
"AMP PEAK  4(3Q26.2) MUTATED" "AMP PEAK  4(3Q26.2) MUTATED" 
                 TCGA-IG-A4P3                  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   4 2
  AMP PEAK  5(5P15.33) WILD-TYPE 6 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                             6                              9 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                             2                              3 
$`AMP PEAK  5(5P15.33) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
        0.03         4.08         3.16        29.00         7.10         0.07 

$`AMP PEAK  5(5P15.33) WILD-TYPE`
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-A4OS TCGA-L5-A4OX TCGA-LN-A4A2 
       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 
                          3.62                           3.48 
[1] "0.0 - 29.0 (3.6)" "0.1 - 30.7 (3.5)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK  5(5P15.33) MUTATED"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-LN-A4A9 
  "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-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK  5(5P15.33) MUTATED"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-LN-A4A9 
  "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-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK  5(5P15.33) MUTATED" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK  5(5P15.33) MUTATED"   "AMP PEAK  5(5P15.33) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK  5(5P15.33) WILD-TYPE" "AMP PEAK  5(5P15.33) WILD-TYPE" 
                    TCGA-LN-A4A9 
  "AMP PEAK  5(5P15.33) MUTATED" 
[1] "hr=" "1.2"
D5V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  5(5P15.33) MUTATED          2         2         2          1
  AMP PEAK  5(5P15.33) WILD-TYPE        0         1         5          3
                                vv
clus                             STAGE IIIB STAGE IIIC
  AMP PEAK  5(5P15.33) MUTATED            0          0
  AMP PEAK  5(5P15.33) WILD-TYPE          2          1
D5V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK  5(5P15.33) MUTATED    2  3     2
  AMP PEAK  5(5P15.33) WILD-TYPE  2  4     6
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                            2                              6
                                vv
clus                             N0 N1+N2+N3
  AMP PEAK  5(5P15.33) MUTATED    4        3
  AMP PEAK  5(5P15.33) WILD-TYPE  3        9
D5V5, multiclass
          clus
vv         AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  N0                                  4                              3
  N1+N2+N3                            3                              9
D5V6, binary
                                cls
clus                              0  1
  AMP PEAK  5(5P15.33) MUTATED    2  5
  AMP PEAK  5(5P15.33) WILD-TYPE  1 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED      2    5
  AMP PEAK  5(5P15.33) WILD-TYPE    1   11
        clus
vv       AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  FEMALE                            2                              1
  MALE                              5                             11
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 5 2
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                            8                             7 
  AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE 
                            3                             2 
$`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-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OU 
        0.03         3.48         3.68         3.32         3.16        29.00 
TCGA-L5-A4OX 
        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                          3.48 
[1] "0.1 - 30.7 (2.7)" "0.0 - 29.0 (3.5)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  6(6P21.1) WILD-TYPE" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  6(6P21.1) MUTATED"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  6(6P21.1) WILD-TYPE" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  6(6P21.1) MUTATED"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK  6(6P21.1) WILD-TYPE" "AMP PEAK  6(6P21.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  6(6P21.1) MUTATED"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  6(6P21.1) WILD-TYPE"   "AMP PEAK  6(6P21.1) MUTATED" 
                   TCGA-LN-A4A9 
  "AMP PEAK  6(6P21.1) MUTATED" 
[1] "hr=" "1.4"
D6V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  6(6P21.1) MUTATED          1         2         3          1
  AMP PEAK  6(6P21.1) WILD-TYPE        1         1         4          3
                               vv
clus                            STAGE IIIB STAGE IIIC
  AMP PEAK  6(6P21.1) MUTATED            1          0
  AMP PEAK  6(6P21.1) WILD-TYPE          1          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     6
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                             6
                               vv
clus                            N0 N1+N2+N3
  AMP PEAK  6(6P21.1) MUTATED    3        5
  AMP PEAK  6(6P21.1) WILD-TYPE  4        7
D6V5, multiclass
          clus
vv         AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  N0                                 3                             4
  N1+N2+N3                           5                             7
D6V6, binary
                               cls
clus                             0  1
  AMP PEAK  6(6P21.1) MUTATED    3  5
  AMP PEAK  6(6P21.1) WILD-TYPE  0 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P21.1) MUTATED      3    5
  AMP PEAK  6(6P21.1) WILD-TYPE    0   11
        clus
vv       AMP PEAK  6(6P21.1) MUTATED AMP PEAK  6(6P21.1) WILD-TYPE
  FEMALE                           3                             0
  MALE                             5                            11
D6V7, continuous

Clustering(7) Variable = AMP PEAK  7(6Q12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                         0 1
  AMP PEAK  7(6Q12) MUTATED   2 3
  AMP PEAK  7(6Q12) WILD-TYPE 8 2
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          5                          10 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          3                           2 
$`AMP PEAK  7(6Q12) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-LN-A4A9 
        0.26        18.35         1.38         7.10         0.07 

$`AMP PEAK  7(6Q12) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         3.48         3.68         4.08         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 
       30.71        29.00         7.43         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 
                       1.38                        3.58 
[1] "0.1 - 18.4 (1.4)" "0.0 - 30.7 (3.6)"
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OE                  TCGA-L5-A4OF 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OR                  TCGA-L5-A4OS 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OU                  TCGA-L5-A4OW 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OX                  TCGA-LN-A4A2 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-LN-A4A9 
  "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OE                  TCGA-L5-A4OF 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OR                  TCGA-L5-A4OS 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OU                  TCGA-L5-A4OW 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OX                  TCGA-LN-A4A2 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-LN-A4A9 
  "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OE                  TCGA-L5-A4OF 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OR                  TCGA-L5-A4OS 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-L5-A4OU                  TCGA-L5-A4OW 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-L5-A4OX                  TCGA-LN-A4A2 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-LN-A4A9 
  "AMP PEAK  7(6Q12) MUTATED" 
[1] "hr=" "3.8"
D7V2, continuous
                             vv
clus                          STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  7(6Q12) MUTATED          0         1         2          2
  AMP PEAK  7(6Q12) WILD-TYPE        2         2         5          2
                             vv
clus                          STAGE IIIB STAGE IIIC
  AMP PEAK  7(6Q12) MUTATED            1          0
  AMP PEAK  7(6Q12) WILD-TYPE          1          1
D7V3, multiclass
                             vv
clus                          T1 T2 T3+T4
  AMP PEAK  7(6Q12) MUTATED    1  3     2
  AMP PEAK  7(6Q12) WILD-TYPE  3  4     6
D7V4, multiclass
       clus
vv      AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  T1                            1                           3
  T2                            3                           4
  T3+T4                         2                           6
                             vv
clus                          N0 N1+N2+N3
  AMP PEAK  7(6Q12) MUTATED    2        4
  AMP PEAK  7(6Q12) WILD-TYPE  5        8
D7V5, multiclass
          clus
vv         AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  N0                               2                           5
  N1+N2+N3                         4                           8
D7V6, binary
                             cls
clus                           0  1
  AMP PEAK  7(6Q12) MUTATED    1  5
  AMP PEAK  7(6Q12) WILD-TYPE  2 11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED      1    5
  AMP PEAK  7(6Q12) WILD-TYPE    2   11
        clus
vv       AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  FEMALE                         1                           2
  MALE                           5                          11
D7V7, continuous

Clustering(8) Variable = AMP PEAK  8(7P11.2) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  8(7P11.2) MUTATED   8 4
  AMP PEAK  8(7P11.2) WILD-TYPE 2 1
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                           12                             3 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                            4                             1 
$`AMP PEAK  8(7P11.2) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         3.48         3.68         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 

$`AMP PEAK  8(7P11.2) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OX TCGA-LN-A4A9 
        0.26         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 
                         3.58                          0.26 
[1] "0.0 - 30.7 (3.6)" "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-L5-A4OE                    TCGA-L5-A4OF 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  8(7P11.2) WILD-TYPE"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  8(7P11.2) WILD-TYPE"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "AMP PEAK  8(7P11.2) MUTATED"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  8(7P11.2) WILD-TYPE"   "AMP PEAK  8(7P11.2) MUTATED" 
                   TCGA-LN-A4A9 
"AMP PEAK  8(7P11.2) WILD-TYPE" 
[1] "hr=" "1.8"
D8V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  8(7P11.2) MUTATED          2         2         6          2
  AMP PEAK  8(7P11.2) WILD-TYPE        0         1         1          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  AMP PEAK  8(7P11.2) MUTATED            1          1
  AMP PEAK  8(7P11.2) WILD-TYPE          1          0
D8V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  8(7P11.2) MUTATED    4  5     5
  AMP PEAK  8(7P11.2) WILD-TYPE  0  2     3
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                           5                             3
                               vv
clus                            N0 N1+N2+N3
  AMP PEAK  8(7P11.2) MUTATED    5        9
  AMP PEAK  8(7P11.2) WILD-TYPE  2        3
D8V5, multiclass
          clus
vv         AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  N0                                 5                             2
  N1+N2+N3                           9                             3
D8V6, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P11.2) MUTATED    3 11
  AMP PEAK  8(7P11.2) WILD-TYPE  0  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED      3   11
  AMP PEAK  8(7P11.2) WILD-TYPE    0    5
        clus
vv       AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  FEMALE                           3                             0
  MALE                            11                             5
D8V7, continuous

Clustering(9) Variable = AMP PEAK  9(7Q21.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  9(7Q21.2) MUTATED   8 4
  AMP PEAK  9(7Q21.2) WILD-TYPE 2 1
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                           12                             3 
  AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE 
                            4                             1 
$`AMP PEAK  9(7Q21.2) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.48         4.08        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.16        30.71        29.00         7.10         0.13         0.07 

$`AMP PEAK  9(7Q21.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OX 
        0.03         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 
                         3.40                          3.68 
[1] "0.1 - 30.7 (3.4)" "0.0 - 7.4 (3.7)" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "AMP PEAK  9(7Q21.2) MUTATED" "AMP PEAK  9(7Q21.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
  "AMP PEAK  9(7Q21.2) MUTATED" "AMP PEAK  9(7Q21.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
  "AMP PEAK  9(7Q21.2) MUTATED" "AMP PEAK  9(7Q21.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "AMP PEAK  9(7Q21.2) MUTATED"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK  9(7Q21.2) WILD-TYPE"   "AMP PEAK  9(7Q21.2) MUTATED" 
                   TCGA-LN-A4A9 
  "AMP PEAK  9(7Q21.2) MUTATED" 
[1] "hr=" "1.3"
D9V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK  9(7Q21.2) MUTATED          2         3         4          2
  AMP PEAK  9(7Q21.2) WILD-TYPE        0         0         3          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  AMP PEAK  9(7Q21.2) MUTATED            2          1
  AMP PEAK  9(7Q21.2) WILD-TYPE          0          0
D9V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  AMP PEAK  9(7Q21.2) MUTATED    3  5     6
  AMP PEAK  9(7Q21.2) WILD-TYPE  1  2     2
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                           6                             2
                               vv
clus                            N0 N1+N2+N3
  AMP PEAK  9(7Q21.2) MUTATED    5        9
  AMP PEAK  9(7Q21.2) WILD-TYPE  2        3
D9V5, multiclass
          clus
vv         AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE
  N0                                 5                             2
  N1+N2+N3                           9                             3
D9V6, binary
                               cls
clus                             0  1
  AMP PEAK  9(7Q21.2) MUTATED    3 11
  AMP PEAK  9(7Q21.2) WILD-TYPE  0  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.2) MUTATED      3   11
  AMP PEAK  9(7Q21.2) WILD-TYPE    0    5
        clus
vv       AMP PEAK  9(7Q21.2) MUTATED AMP PEAK  9(7Q21.2) WILD-TYPE
  FEMALE                           3                             0
  MALE                            11                             5
D9V7, continuous

Clustering(10) Variable = AMP PEAK 10(8P11.21) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 10(8P11.21) MUTATED   6 4
  AMP PEAK 10(8P11.21) WILD-TYPE 4 1
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                            10                              5 
  AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE 
                             4                              1 
$`AMP PEAK 10(8P11.21) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.68         4.08        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 10(8P11.21) WILD-TYPE`
TCGA-L5-A4OE TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-LN-A4A2 
        3.48         1.38        30.71        29.00         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 
                          3.50                           3.48 
[1] "0.0 - 18.4 (3.5)" "0.1 - 30.7 (3.5)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-LN-A4A9 
  "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-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-LN-A4A9 
  "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-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 10(8P11.21) MUTATED"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 10(8P11.21) WILD-TYPE"   "AMP PEAK 10(8P11.21) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "AMP PEAK 10(8P11.21) MUTATED" "AMP PEAK 10(8P11.21) WILD-TYPE" 
                    TCGA-LN-A4A9 
  "AMP PEAK 10(8P11.21) MUTATED" 
[1] "hr=" "3.5"
D10V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 10(8P11.21) MUTATED          2         1         6          1
  AMP PEAK 10(8P11.21) WILD-TYPE        0         2         1          3
                                vv
clus                             STAGE IIIB STAGE IIIC
  AMP PEAK 10(8P11.21) MUTATED            1          1
  AMP PEAK 10(8P11.21) WILD-TYPE          1          0
D10V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 10(8P11.21) MUTATED    4  5     3
  AMP PEAK 10(8P11.21) WILD-TYPE  0  2     5
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                            3                              5
                                vv
clus                             N0 N1+N2+N3
  AMP PEAK 10(8P11.21) MUTATED    4        8
  AMP PEAK 10(8P11.21) WILD-TYPE  3        4
D10V5, multiclass
          clus
vv         AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE
  N0                                  4                              3
  N1+N2+N3                            8                              4
D10V6, binary
                                cls
clus                              0  1
  AMP PEAK 10(8P11.21) MUTATED    2 10
  AMP PEAK 10(8P11.21) WILD-TYPE  1  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.21) MUTATED      2   10
  AMP PEAK 10(8P11.21) WILD-TYPE    1    6
        clus
vv       AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE
  FEMALE                            2                              1
  MALE                             10                              6
D10V7, continuous

Clustering(11) Variable = AMP PEAK 11(8Q24.21) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 11(8Q24.21) MUTATED   7 5
  AMP PEAK 11(8Q24.21) WILD-TYPE 3 0
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            12                              3 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                             5                              0 
$`AMP PEAK 11(8Q24.21) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.48         4.08        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.16        30.71         7.10         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 
                          3.40                           3.68 
[1] "0.1 - 30.7 (3.4)" "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-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-LN-A4A9 
  "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-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-LN-A4A9 
  "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-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-LN-A4A9 
  "AMP PEAK 11(8Q24.21) MUTATED" 
[1] "hr="     "7.7e+08"
D11V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 11(8Q24.21) MUTATED          2         2         5          4
  AMP PEAK 11(8Q24.21) WILD-TYPE        0         1         2          0
                                vv
clus                             STAGE IIIB STAGE IIIC
  AMP PEAK 11(8Q24.21) MUTATED            2          1
  AMP PEAK 11(8Q24.21) WILD-TYPE          0          0
D11V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 11(8Q24.21) MUTATED    3  6     7
  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                            7                              1
                                vv
clus                             N0 N1+N2+N3
  AMP PEAK 11(8Q24.21) MUTATED    6       10
  AMP PEAK 11(8Q24.21) WILD-TYPE  1        2
D11V5, multiclass
          clus
vv         AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  N0                                  6                              1
  N1+N2+N3                           10                              2
D11V6, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q24.21) MUTATED    3 13
  AMP PEAK 11(8Q24.21) WILD-TYPE  0  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED      3   13
  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                             13                              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 
                            10                              2 
                  TCGA-IG-A3Y9                   TCGA-IG-A3YA 
"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 13(11P13) MUTATION ANALYSIS
D12V1, survival
                              sevent
clus2                          0 1
  AMP PEAK 13(11P13) MUTATED   3 1
  AMP PEAK 13(11P13) WILD-TYPE 7 4
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                           4                           11 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                           1                            4 
$`AMP PEAK 13(11P13) MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OU 
        3.48         4.08        18.35        29.00 

$`AMP PEAK 13(11P13) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.03         0.26         3.68         3.32         1.38         3.16 
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 

  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                        3.48                         0.03 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                       29.00                        30.71 
  AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE 
                      11.215                        3.160 
[1] "3.5 - 29.0 (11.2)" "0.0 - 30.7 (3.2)" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
  "AMP PEAK 13(11P13) MUTATED" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
  "AMP PEAK 13(11P13) MUTATED"   "AMP PEAK 13(11P13) MUTATED" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
  "AMP PEAK 13(11P13) MUTATED" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-LN-A4A9 
"AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
  "AMP PEAK 13(11P13) MUTATED" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
  "AMP PEAK 13(11P13) MUTATED"   "AMP PEAK 13(11P13) MUTATED" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
  "AMP PEAK 13(11P13) MUTATED" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-LN-A4A9 
"AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
  "AMP PEAK 13(11P13) MUTATED" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
  "AMP PEAK 13(11P13) MUTATED"   "AMP PEAK 13(11P13) MUTATED" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
  "AMP PEAK 13(11P13) MUTATED" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"AMP PEAK 13(11P13) WILD-TYPE" "AMP PEAK 13(11P13) WILD-TYPE" 
                  TCGA-LN-A4A9 
"AMP PEAK 13(11P13) WILD-TYPE" 
[1] "hr=" "3.7"
D12V2, continuous
                              vv
clus                           STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 13(11P13) MUTATED          1         1         1          0
  AMP PEAK 13(11P13) WILD-TYPE        1         2         6          4
                              vv
clus                           STAGE IIIB STAGE IIIC
  AMP PEAK 13(11P13) MUTATED            1          0
  AMP PEAK 13(11P13) WILD-TYPE          1          1
D12V3, multiclass
                              vv
clus                           T1 T2 T3+T4
  AMP PEAK 13(11P13) MUTATED    2  0     2
  AMP PEAK 13(11P13) WILD-TYPE  2  7     6
D12V4, multiclass
       clus
vv      AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  T1                             2                            2
  T2                             0                            7
  T3+T4                          2                            6
                              vv
clus                           N0 N1+N2+N3
  AMP PEAK 13(11P13) MUTATED    2        2
  AMP PEAK 13(11P13) WILD-TYPE  5       10
D12V5, multiclass
          clus
vv         AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  N0                                2                            5
  N1+N2+N3                          2                           10
D12V6, binary
                              cls
clus                            0  1
  AMP PEAK 13(11P13) MUTATED    1  3
  AMP PEAK 13(11P13) WILD-TYPE  2 13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(11P13) MUTATED      1    3
  AMP PEAK 13(11P13) WILD-TYPE    2   13
        clus
vv       AMP PEAK 13(11P13) MUTATED AMP PEAK 13(11P13) WILD-TYPE
  FEMALE                          1                            2
  MALE                            3                           13
D12V7, continuous

Clustering(13) Variable = AMP PEAK 14(11Q13.3) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 14(11Q13.3) MUTATED   7 1
  AMP PEAK 14(11Q13.3) WILD-TYPE 3 4
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                             8                              7 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                             1                              4 
$`AMP PEAK 14(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 14(11Q13.3) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX 
        0.26        18.35         3.32         3.16         7.10         7.43 
TCGA-LN-A4A9 
        0.07 

  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                         30.71                          18.35 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                          3.58                           3.32 
[1] "0.0 - 30.7 (3.6)" "0.1 - 18.4 (3.3)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 14(11Q13.3) MUTATED" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 14(11Q13.3) MUTATED"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 14(11Q13.3) MUTATED" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 14(11Q13.3) WILD-TYPE"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"AMP PEAK 14(11Q13.3) WILD-TYPE"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK 14(11Q13.3) MUTATED" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 14(11Q13.3) WILD-TYPE"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-LN-A4A9 
"AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 14(11Q13.3) MUTATED" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 14(11Q13.3) MUTATED"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 14(11Q13.3) MUTATED" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 14(11Q13.3) WILD-TYPE"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"AMP PEAK 14(11Q13.3) WILD-TYPE"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK 14(11Q13.3) MUTATED" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 14(11Q13.3) WILD-TYPE"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-LN-A4A9 
"AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 14(11Q13.3) MUTATED" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 14(11Q13.3) MUTATED"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 14(11Q13.3) MUTATED" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 14(11Q13.3) WILD-TYPE"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"AMP PEAK 14(11Q13.3) WILD-TYPE"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK 14(11Q13.3) MUTATED" "AMP PEAK 14(11Q13.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 14(11Q13.3) WILD-TYPE"   "AMP PEAK 14(11Q13.3) MUTATED" 
                    TCGA-LN-A4A9 
"AMP PEAK 14(11Q13.3) WILD-TYPE" 
[1] "hr=" "4.6"
D13V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 14(11Q13.3) MUTATED          1         2         4          3
  AMP PEAK 14(11Q13.3) WILD-TYPE        1         1         3          1
                                vv
clus                             STAGE IIIB STAGE IIIC
  AMP PEAK 14(11Q13.3) MUTATED            1          0
  AMP PEAK 14(11Q13.3) WILD-TYPE          1          1
D13V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 14(11Q13.3) MUTATED    2  4     5
  AMP PEAK 14(11Q13.3) WILD-TYPE  2  3     3
D13V4, multiclass
       clus
vv      AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  T1                               2                              2
  T2                               4                              3
  T3+T4                            5                              3
                                vv
clus                             N0 N1+N2+N3
  AMP PEAK 14(11Q13.3) MUTATED    5        6
  AMP PEAK 14(11Q13.3) WILD-TYPE  2        6
D13V5, multiclass
          clus
vv         AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  N0                                  5                              2
  N1+N2+N3                            6                              6
D13V6, binary
                                cls
clus                             0 1
  AMP PEAK 14(11Q13.3) MUTATED   2 9
  AMP PEAK 14(11Q13.3) WILD-TYPE 1 7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      2    9
  AMP PEAK 14(11Q13.3) WILD-TYPE    1    7
        clus
vv       AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  FEMALE                            2                              1
  MALE                              9                              7
D13V7, continuous

Clustering(14) Variable = AMP PEAK 15(12P13.33) MUTATION ANALYSIS
D14V1, survival
                                 sevent
clus2                             0 1
  AMP PEAK 15(12P13.33) MUTATED   5 1
  AMP PEAK 15(12P13.33) WILD-TYPE 5 4
  AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE 
                              6                               9 
  AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE 
                              1                               4 
$`AMP PEAK 15(12P13.33) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-LN-A4A2 
        0.03         3.48         4.08         3.32         3.16         0.13 

$`AMP PEAK 15(12P13.33) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        0.26         3.68        18.35         1.38        30.71        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        7.10         7.43         0.07 

  AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE 
                           0.03                            0.07 
  AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE 
                           4.08                           30.71 
  AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE 
                           3.24                            7.10 
[1] "0.0 - 4.1 (3.2)"  "0.1 - 30.7 (7.1)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"AMP PEAK 15(12P13.33) WILD-TYPE" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"AMP PEAK 15(12P13.33) WILD-TYPE"   "AMP PEAK 15(12P13.33) MUTATED" 
                     TCGA-LN-A4A9 
"AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"AMP PEAK 15(12P13.33) WILD-TYPE" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"AMP PEAK 15(12P13.33) WILD-TYPE"   "AMP PEAK 15(12P13.33) MUTATED" 
                     TCGA-LN-A4A9 
"AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "AMP PEAK 15(12P13.33) MUTATED" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"AMP PEAK 15(12P13.33) WILD-TYPE" "AMP PEAK 15(12P13.33) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"AMP PEAK 15(12P13.33) WILD-TYPE"   "AMP PEAK 15(12P13.33) MUTATED" 
                     TCGA-LN-A4A9 
"AMP PEAK 15(12P13.33) WILD-TYPE" 
[1] "hr=" "1.6"
D14V2, continuous
                                 vv
clus                              STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 15(12P13.33) MUTATED          2         1         1          2
  AMP PEAK 15(12P13.33) WILD-TYPE        0         2         6          2
                                 vv
clus                              STAGE IIIB STAGE IIIC
  AMP PEAK 15(12P13.33) MUTATED            1          1
  AMP PEAK 15(12P13.33) WILD-TYPE          1          0
D14V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  AMP PEAK 15(12P13.33) MUTATED    2  1     5
  AMP PEAK 15(12P13.33) WILD-TYPE  2  6     3
D14V4, multiclass
       clus
vv      AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE
  T1                                2                               2
  T2                                1                               6
  T3+T4                             5                               3
                                 vv
clus                              N0 N1+N2+N3
  AMP PEAK 15(12P13.33) MUTATED    4        4
  AMP PEAK 15(12P13.33) WILD-TYPE  3        8
D14V5, multiclass
          clus
vv         AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE
  N0                                   4                               3
  N1+N2+N3                             4                               8
D14V6, binary
                                 cls
clus                              0 1
  AMP PEAK 15(12P13.33) MUTATED   1 7
  AMP PEAK 15(12P13.33) WILD-TYPE 2 9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(12P13.33) MUTATED      1    7
  AMP PEAK 15(12P13.33) WILD-TYPE    2    9
        clus
vv       AMP PEAK 15(12P13.33) MUTATED AMP PEAK 15(12P13.33) WILD-TYPE
  FEMALE                             1                               2
  MALE                               7                               9
D14V7, continuous

Clustering(15) Variable = AMP PEAK 16(12P12.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 16(12P12.1) MUTATED   6 1
  AMP PEAK 16(12P12.1) WILD-TYPE 4 4
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                             7                              8 
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                             1                              4 
$`AMP PEAK 16(12P12.1) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.48         4.08        18.35         3.32 
TCGA-L5-A4OU 
       29.00 

$`AMP PEAK 16(12P12.1) WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        3.68         1.38         3.16        30.71         7.10         7.43 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                         29.00                          30.71 
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                          3.48                           3.42 
[1] "0.0 - 29.0 (3.5)" "0.1 - 30.7 (3.4)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 16(12P12.1) MUTATED"   "AMP PEAK 16(12P12.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 16(12P12.1) MUTATED" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 16(12P12.1) MUTATED"   "AMP PEAK 16(12P12.1) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 16(12P12.1) MUTATED" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"AMP PEAK 16(12P12.1) WILD-TYPE" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK 16(12P12.1) MUTATED" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 16(12P12.1) WILD-TYPE" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 16(12P12.1) MUTATED"   "AMP PEAK 16(12P12.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 16(12P12.1) MUTATED" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 16(12P12.1) MUTATED"   "AMP PEAK 16(12P12.1) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 16(12P12.1) MUTATED" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"AMP PEAK 16(12P12.1) WILD-TYPE" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK 16(12P12.1) MUTATED" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 16(12P12.1) WILD-TYPE" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 16(12P12.1) MUTATED"   "AMP PEAK 16(12P12.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 16(12P12.1) MUTATED" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "AMP PEAK 16(12P12.1) MUTATED"   "AMP PEAK 16(12P12.1) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 16(12P12.1) MUTATED" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"AMP PEAK 16(12P12.1) WILD-TYPE" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK 16(12P12.1) MUTATED" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 16(12P12.1) WILD-TYPE" "AMP PEAK 16(12P12.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 16(12P12.1) WILD-TYPE" 
[1] "hr=" "4.3"
D15V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 16(12P12.1) MUTATED          1         1         2          1
  AMP PEAK 16(12P12.1) WILD-TYPE        1         2         5          3
                                vv
clus                             STAGE IIIB STAGE IIIC
  AMP PEAK 16(12P12.1) MUTATED            2          1
  AMP PEAK 16(12P12.1) WILD-TYPE          0          0
D15V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 16(12P12.1) MUTATED    2  1     5
  AMP PEAK 16(12P12.1) WILD-TYPE  2  6     3
D15V4, multiclass
       clus
vv      AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  T1                               2                              2
  T2                               1                              6
  T3+T4                            5                              3
                                vv
clus                             N0 N1+N2+N3
  AMP PEAK 16(12P12.1) MUTATED    2        6
  AMP PEAK 16(12P12.1) WILD-TYPE  5        6
D15V5, multiclass
          clus
vv         AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  N0                                  2                              5
  N1+N2+N3                            6                              6
D15V6, binary
                                cls
clus                             0 1
  AMP PEAK 16(12P12.1) MUTATED   1 7
  AMP PEAK 16(12P12.1) WILD-TYPE 2 9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(12P12.1) MUTATED      1    7
  AMP PEAK 16(12P12.1) WILD-TYPE    2    9
        clus
vv       AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  FEMALE                            1                              2
  MALE                              7                              9
D15V7, continuous

Clustering(16) Variable = AMP PEAK 17(14Q22.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 17(14Q22.1) MUTATED   2 2
  AMP PEAK 17(14Q22.1) WILD-TYPE 8 3
  AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE 
                             4                             11 
  AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE 
                             2                              3 
$`AMP PEAK 17(14Q22.1) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OR TCGA-L5-A4OW TCGA-LN-A4A9 
        0.03         3.16         7.10         0.07 

$`AMP PEAK 17(14Q22.1) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.48         3.68         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38        30.71        29.00         7.43         0.13 

  AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE 
                          0.03                           0.13 
  AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE 
                          7.10                          30.71 
  AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE 
                         1.615                          3.680 
[1] "0.0 - 7.1 (1.6)"  "0.1 - 30.7 (3.7)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 17(14Q22.1) MUTATED" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 17(14Q22.1) MUTATED" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 17(14Q22.1) WILD-TYPE"   "AMP PEAK 17(14Q22.1) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
  "AMP PEAK 17(14Q22.1) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 17(14Q22.1) MUTATED" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 17(14Q22.1) MUTATED" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 17(14Q22.1) WILD-TYPE"   "AMP PEAK 17(14Q22.1) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
  "AMP PEAK 17(14Q22.1) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 17(14Q22.1) MUTATED" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 17(14Q22.1) MUTATED" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 17(14Q22.1) WILD-TYPE"   "AMP PEAK 17(14Q22.1) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 17(14Q22.1) WILD-TYPE" "AMP PEAK 17(14Q22.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
  "AMP PEAK 17(14Q22.1) MUTATED" 
[1] "hr=" "8.3"
D16V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 17(14Q22.1) MUTATED          1         1         2          2
  AMP PEAK 17(14Q22.1) WILD-TYPE        1         2         5          2
                                vv
clus                             STAGE IIIB STAGE IIIC
  AMP PEAK 17(14Q22.1) MUTATED            0          0
  AMP PEAK 17(14Q22.1) WILD-TYPE          2          1
D16V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 17(14Q22.1) MUTATED    1  3     2
  AMP PEAK 17(14Q22.1) WILD-TYPE  3  4     6
D16V4, multiclass
       clus
vv      AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE
  T1                               1                              3
  T2                               3                              4
  T3+T4                            2                              6
                                vv
clus                             N0 N1+N2+N3
  AMP PEAK 17(14Q22.1) MUTATED    4        2
  AMP PEAK 17(14Q22.1) WILD-TYPE  3       10
D16V5, multiclass
          clus
vv         AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE
  N0                                  4                              3
  N1+N2+N3                            2                             10
D16V6, binary
                                cls
clus                              0  1
  AMP PEAK 17(14Q22.1) MUTATED    1  5
  AMP PEAK 17(14Q22.1) WILD-TYPE  2 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(14Q22.1) MUTATED      1    5
  AMP PEAK 17(14Q22.1) WILD-TYPE    2   11
        clus
vv       AMP PEAK 17(14Q22.1) MUTATED AMP PEAK 17(14Q22.1) WILD-TYPE
  FEMALE                            1                              2
  MALE                              5                             11
D16V7, continuous

Clustering(17) Variable = AMP PEAK 18(17Q12) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                          0 1
  AMP PEAK 18(17Q12) MUTATED   5 3
  AMP PEAK 18(17Q12) WILD-TYPE 5 2
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                           8                            7 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                           3                            2 
$`AMP PEAK 18(17Q12) MUTATED`
TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        3.48        18.35         3.32         1.38        30.71        29.00 
TCGA-L5-A4OW TCGA-LN-A4A2 
        7.10         0.13 

$`AMP PEAK 18(17Q12) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OX 
        0.03         0.26         3.68         4.08         3.16         7.43 
TCGA-LN-A4A9 
        0.07 

  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                        0.13                         0.03 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                       30.71                         7.43 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                        5.29                         3.16 
[1] "0.1 - 30.7 (5.3)" "0.0 - 7.4 (3.2)" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 18(17Q12) WILD-TYPE" "AMP PEAK 18(17Q12) WILD-TYPE" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
  "AMP PEAK 18(17Q12) MUTATED" "AMP PEAK 18(17Q12) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"AMP PEAK 18(17Q12) WILD-TYPE"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
  "AMP PEAK 18(17Q12) MUTATED"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
"AMP PEAK 18(17Q12) WILD-TYPE"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
  "AMP PEAK 18(17Q12) MUTATED"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"AMP PEAK 18(17Q12) WILD-TYPE"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-LN-A4A9 
"AMP PEAK 18(17Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 18(17Q12) WILD-TYPE" "AMP PEAK 18(17Q12) WILD-TYPE" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
  "AMP PEAK 18(17Q12) MUTATED" "AMP PEAK 18(17Q12) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"AMP PEAK 18(17Q12) WILD-TYPE"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
  "AMP PEAK 18(17Q12) MUTATED"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
"AMP PEAK 18(17Q12) WILD-TYPE"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
  "AMP PEAK 18(17Q12) MUTATED"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"AMP PEAK 18(17Q12) WILD-TYPE"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-LN-A4A9 
"AMP PEAK 18(17Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 18(17Q12) WILD-TYPE" "AMP PEAK 18(17Q12) WILD-TYPE" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
  "AMP PEAK 18(17Q12) MUTATED" "AMP PEAK 18(17Q12) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"AMP PEAK 18(17Q12) WILD-TYPE"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
  "AMP PEAK 18(17Q12) MUTATED"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
"AMP PEAK 18(17Q12) WILD-TYPE"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
  "AMP PEAK 18(17Q12) MUTATED"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"AMP PEAK 18(17Q12) WILD-TYPE"   "AMP PEAK 18(17Q12) MUTATED" 
                  TCGA-LN-A4A9 
"AMP PEAK 18(17Q12) WILD-TYPE" 
[1] "hr=" "2.4"
D17V2, continuous
                              vv
clus                           STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 18(17Q12) MUTATED          0         2         4          1
  AMP PEAK 18(17Q12) WILD-TYPE        2         1         3          3
                              vv
clus                           STAGE IIIB STAGE IIIC
  AMP PEAK 18(17Q12) MUTATED            1          1
  AMP PEAK 18(17Q12) WILD-TYPE          1          0
D17V3, multiclass
                              vv
clus                           T1 T2 T3+T4
  AMP PEAK 18(17Q12) MUTATED    1  4     4
  AMP PEAK 18(17Q12) WILD-TYPE  3  3     4
D17V4, multiclass
       clus
vv      AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  T1                             1                            3
  T2                             4                            3
  T3+T4                          4                            4
                              vv
clus                           N0 N1+N2+N3
  AMP PEAK 18(17Q12) MUTATED    2        7
  AMP PEAK 18(17Q12) WILD-TYPE  5        5
D17V5, multiclass
          clus
vv         AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  N0                                2                            5
  N1+N2+N3                          7                            5
D17V6, binary
                              cls
clus                           0 1
  AMP PEAK 18(17Q12) MUTATED   2 7
  AMP PEAK 18(17Q12) WILD-TYPE 1 9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED      2    7
  AMP PEAK 18(17Q12) WILD-TYPE    1    9
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  FEMALE                          2                            1
  MALE                            7                            9
D17V7, continuous

Clustering(18) Variable = AMP PEAK 19(17Q24.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 19(17Q24.3) MUTATED   6 2
  AMP PEAK 19(17Q24.3) WILD-TYPE 4 3
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                             8                              7 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                             2                              3 
$`AMP PEAK 19(17Q24.3) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU 
        0.03         3.48        18.35         3.32         1.38        29.00 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

$`AMP PEAK 19(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 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                          0.03                           0.26 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                         29.00                          30.71 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                          2.35                           4.08 
[1] "0.0 - 29.0 (2.3)" "0.3 - 30.7 (4.1)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 19(17Q24.3) MUTATED" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 19(17Q24.3) MUTATED" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 19(17Q24.3) WILD-TYPE"   "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 19(17Q24.3) MUTATED"   "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"AMP PEAK 19(17Q24.3) WILD-TYPE" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK 19(17Q24.3) MUTATED" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 19(17Q24.3) WILD-TYPE"   "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-LN-A4A9 
  "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 19(17Q24.3) MUTATED" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 19(17Q24.3) MUTATED" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 19(17Q24.3) WILD-TYPE"   "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 19(17Q24.3) MUTATED"   "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"AMP PEAK 19(17Q24.3) WILD-TYPE" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK 19(17Q24.3) MUTATED" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 19(17Q24.3) WILD-TYPE"   "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-LN-A4A9 
  "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 19(17Q24.3) MUTATED" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 19(17Q24.3) MUTATED" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 19(17Q24.3) WILD-TYPE"   "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 19(17Q24.3) MUTATED"   "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"AMP PEAK 19(17Q24.3) WILD-TYPE" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "AMP PEAK 19(17Q24.3) MUTATED" "AMP PEAK 19(17Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 19(17Q24.3) WILD-TYPE"   "AMP PEAK 19(17Q24.3) MUTATED" 
                    TCGA-LN-A4A9 
  "AMP PEAK 19(17Q24.3) MUTATED" 
[1] "hr=" "1.4"
D18V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 19(17Q24.3) MUTATED          0         3         3          1
  AMP PEAK 19(17Q24.3) WILD-TYPE        2         0         4          3
                                vv
clus                             STAGE IIIB STAGE IIIC
  AMP PEAK 19(17Q24.3) MUTATED            1          1
  AMP PEAK 19(17Q24.3) WILD-TYPE          1          0
D18V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 19(17Q24.3) MUTATED    1  4     4
  AMP PEAK 19(17Q24.3) WILD-TYPE  3  3     4
D18V4, multiclass
       clus
vv      AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE
  T1                               1                              3
  T2                               4                              3
  T3+T4                            4                              4
                                vv
clus                             N0 N1+N2+N3
  AMP PEAK 19(17Q24.3) MUTATED    3        6
  AMP PEAK 19(17Q24.3) WILD-TYPE  4        6
D18V5, multiclass
          clus
vv         AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE
  N0                                  3                              4
  N1+N2+N3                            6                              6
D18V6, binary
                                cls
clus                             0 1
  AMP PEAK 19(17Q24.3) MUTATED   0 9
  AMP PEAK 19(17Q24.3) WILD-TYPE 3 7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.3) MUTATED      0    9
  AMP PEAK 19(17Q24.3) WILD-TYPE    3    7
        clus
vv       AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE
  FEMALE                            0                              3
  MALE                              9                              7
D18V7, continuous

Clustering(19) Variable = AMP PEAK 20(18P11.32) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                             0 1
  AMP PEAK 20(18P11.32) MUTATED   2 3
  AMP PEAK 20(18P11.32) WILD-TYPE 8 2
  AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE 
                              5                              10 
  AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE 
                              3                               2 
$`AMP PEAK 20(18P11.32) MUTATED`
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW 
        4.08         3.32         1.38         3.16         7.10 

$`AMP PEAK 20(18P11.32) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OS 
        0.03         0.26         3.48         3.68        18.35        30.71 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       29.00         7.43         0.13         0.07 

  AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE 
                           1.38                            0.03 
  AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE 
                           7.10                           30.71 
  AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE 
                           3.32                            3.58 
[1] "1.4 - 7.1 (3.3)"  "0.0 - 30.7 (3.6)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"AMP PEAK 20(18P11.32) WILD-TYPE" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"AMP PEAK 20(18P11.32) WILD-TYPE" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "AMP PEAK 20(18P11.32) MUTATED" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "AMP PEAK 20(18P11.32) MUTATED"   "AMP PEAK 20(18P11.32) MUTATED" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "AMP PEAK 20(18P11.32) MUTATED" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"AMP PEAK 20(18P11.32) WILD-TYPE"   "AMP PEAK 20(18P11.32) MUTATED" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"AMP PEAK 20(18P11.32) WILD-TYPE" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-LN-A4A9 
"AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"AMP PEAK 20(18P11.32) WILD-TYPE" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"AMP PEAK 20(18P11.32) WILD-TYPE" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "AMP PEAK 20(18P11.32) MUTATED" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "AMP PEAK 20(18P11.32) MUTATED"   "AMP PEAK 20(18P11.32) MUTATED" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "AMP PEAK 20(18P11.32) MUTATED" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"AMP PEAK 20(18P11.32) WILD-TYPE"   "AMP PEAK 20(18P11.32) MUTATED" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"AMP PEAK 20(18P11.32) WILD-TYPE" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-LN-A4A9 
"AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"AMP PEAK 20(18P11.32) WILD-TYPE" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"AMP PEAK 20(18P11.32) WILD-TYPE" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "AMP PEAK 20(18P11.32) MUTATED" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "AMP PEAK 20(18P11.32) MUTATED"   "AMP PEAK 20(18P11.32) MUTATED" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "AMP PEAK 20(18P11.32) MUTATED" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"AMP PEAK 20(18P11.32) WILD-TYPE"   "AMP PEAK 20(18P11.32) MUTATED" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"AMP PEAK 20(18P11.32) WILD-TYPE" "AMP PEAK 20(18P11.32) WILD-TYPE" 
                     TCGA-LN-A4A9 
"AMP PEAK 20(18P11.32) WILD-TYPE" 
[1] "hr="     "4.4e+09"
D19V2, continuous
                                 vv
clus                              STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 20(18P11.32) MUTATED          2         0         1          1
  AMP PEAK 20(18P11.32) WILD-TYPE        0         3         6          3
                                 vv
clus                              STAGE IIIB STAGE IIIC
  AMP PEAK 20(18P11.32) MUTATED            0          1
  AMP PEAK 20(18P11.32) WILD-TYPE          2          0
D19V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  AMP PEAK 20(18P11.32) MUTATED    2  2     1
  AMP PEAK 20(18P11.32) WILD-TYPE  2  5     7
D19V4, multiclass
       clus
vv      AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE
  T1                                2                               2
  T2                                2                               5
  T3+T4                             1                               7
                                 vv
clus                              N0 N1+N2+N3
  AMP PEAK 20(18P11.32) MUTATED    2        3
  AMP PEAK 20(18P11.32) WILD-TYPE  5        9
D19V5, multiclass
          clus
vv         AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE
  N0                                   2                               5
  N1+N2+N3                             3                               9
D19V6, binary
                                 cls
clus                               0  1
  AMP PEAK 20(18P11.32) MUTATED    2  3
  AMP PEAK 20(18P11.32) WILD-TYPE  1 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(18P11.32) MUTATED      2    3
  AMP PEAK 20(18P11.32) WILD-TYPE    1   13
        clus
vv       AMP PEAK 20(18P11.32) MUTATED AMP PEAK 20(18P11.32) WILD-TYPE
  FEMALE                             2                               1
  MALE                               3                              13
D19V7, continuous

Clustering(20) Variable = AMP PEAK 21(18Q11.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 21(18Q11.2) MUTATED   3 2
  AMP PEAK 21(18Q11.2) WILD-TYPE 7 3
  AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE 
                             5                             10 
  AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE 
                             2                              3 
$`AMP PEAK 21(18Q11.2) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         3.48        18.35         3.32         3.16 

$`AMP PEAK 21(18Q11.2) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        0.26         3.68         4.08         1.38        30.71        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        7.10         7.43         0.13         0.07 

  AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE 
                         18.35                          30.71 
  AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE 
                          3.32                           3.88 
[1] "0.0 - 18.4 (3.3)" "0.1 - 30.7 (3.9)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 21(18Q11.2) WILD-TYPE"   "AMP PEAK 21(18Q11.2) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 21(18Q11.2) WILD-TYPE" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 21(18Q11.2) WILD-TYPE" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 21(18Q11.2) WILD-TYPE"   "AMP PEAK 21(18Q11.2) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 21(18Q11.2) WILD-TYPE" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 21(18Q11.2) WILD-TYPE" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 21(18Q11.2) WILD-TYPE"   "AMP PEAK 21(18Q11.2) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 21(18Q11.2) MUTATED" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 21(18Q11.2) WILD-TYPE" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 21(18Q11.2) WILD-TYPE" "AMP PEAK 21(18Q11.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 21(18Q11.2) WILD-TYPE" 
[1] "hr=" "1.5"
D20V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 21(18Q11.2) MUTATED          1         0         2          0
  AMP PEAK 21(18Q11.2) WILD-TYPE        1         3         5          4
                                vv
clus                             STAGE IIIB STAGE IIIC
  AMP PEAK 21(18Q11.2) MUTATED            1          1
  AMP PEAK 21(18Q11.2) WILD-TYPE          1          0
D20V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 21(18Q11.2) MUTATED    2  1     2
  AMP PEAK 21(18Q11.2) WILD-TYPE  2  6     6
D20V4, multiclass
       clus
vv      AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE
  T1                               2                              2
  T2                               1                              6
  T3+T4                            2                              6
                                vv
clus                             N0 N1+N2+N3
  AMP PEAK 21(18Q11.2) MUTATED    1        4
  AMP PEAK 21(18Q11.2) WILD-TYPE  6        8
D20V5, multiclass
          clus
vv         AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE
  N0                                  1                              6
  N1+N2+N3                            4                              8
D20V6, binary
                                cls
clus                              0  1
  AMP PEAK 21(18Q11.2) MUTATED    0  5
  AMP PEAK 21(18Q11.2) WILD-TYPE  3 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(18Q11.2) MUTATED      0    5
  AMP PEAK 21(18Q11.2) WILD-TYPE    3   11
        clus
vv       AMP PEAK 21(18Q11.2) MUTATED AMP PEAK 21(18Q11.2) WILD-TYPE
  FEMALE                            0                              3
  MALE                              5                             11
D20V7, continuous

Clustering(21) Variable = AMP PEAK 22(19P13.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 22(19P13.2) MUTATED   1 1
  AMP PEAK 22(19P13.2) WILD-TYPE 9 4
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                             2                             13 
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                             1                              4 
$`AMP PEAK 22(19P13.2) MUTATED`
TCGA-L5-A4OR TCGA-L5-A4OS 
        3.16        30.71 

$`AMP PEAK 22(19P13.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         3.48         3.68         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        3.32         1.38        29.00         7.10         7.43         0.13 
TCGA-LN-A4A9 
        0.07 

  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                          3.16                           0.03 
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                         30.71                          29.00 
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                        16.935                          3.480 
[1] "3.2 - 30.7 (16.9)" "0.0 - 29.0 (3.5)" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 22(19P13.2) MUTATED"   "AMP PEAK 22(19P13.2) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 22(19P13.2) MUTATED"   "AMP PEAK 22(19P13.2) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "AMP PEAK 22(19P13.2) MUTATED"   "AMP PEAK 22(19P13.2) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 22(19P13.2) WILD-TYPE" 
[1] "Remove cluster labels:"       "AMP PEAK 22(19P13.2) MUTATED"
clus
  AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE 
                             2                             13 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"AMP PEAK 22(19P13.2) WILD-TYPE" "AMP PEAK 22(19P13.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"AMP PEAK 22(19P13.2) WILD-TYPE" 
D21V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 22(19P13.2) MUTATED          1         0         2          0
  AMP PEAK 22(19P13.2) WILD-TYPE        1         3         5          4
                                vv
clus                             STAGE IIIB STAGE IIIC
  AMP PEAK 22(19P13.2) MUTATED            0          0
  AMP PEAK 22(19P13.2) WILD-TYPE          2          1
D21V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  AMP PEAK 22(19P13.2) MUTATED    1  2     0
  AMP PEAK 22(19P13.2) WILD-TYPE  3  5     8
D21V4, multiclass
       clus
vv      AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  T1                               1                              3
  T2                               2                              5
  T3+T4                            0                              8
                                vv
clus                             N0 N1+N2+N3
  AMP PEAK 22(19P13.2) MUTATED    1        2
  AMP PEAK 22(19P13.2) WILD-TYPE  6       10
D21V5, multiclass
          clus
vv         AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  N0                                  1                              6
  N1+N2+N3                            2                             10
D21V6, binary
                                cls
clus                              0  1
  AMP PEAK 22(19P13.2) MUTATED    1  2
  AMP PEAK 22(19P13.2) WILD-TYPE  2 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(19P13.2) MUTATED      1    2
  AMP PEAK 22(19P13.2) WILD-TYPE    2   14
        clus
vv       AMP PEAK 22(19P13.2) MUTATED AMP PEAK 22(19P13.2) WILD-TYPE
  FEMALE                            1                              2
  MALE                              2                             14
D21V7, continuous

Clustering(22) Variable = AMP PEAK 23(19P13.11) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                             0 1
  AMP PEAK 23(19P13.11) MUTATED   1 3
  AMP PEAK 23(19P13.11) WILD-TYPE 9 2
  AMP PEAK 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE 
                              4                              11 
  AMP PEAK 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE 
                              3                               2 
$`AMP PEAK 23(19P13.11) MUTATED`
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       18.35         3.32         1.38         3.16 

$`AMP PEAK 23(19P13.11) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS 
        0.03         0.26         3.48         3.68         4.08        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 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE 
                           1.38                            0.03 
  AMP PEAK 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE 
                          18.35                           30.71 
  AMP PEAK 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE 
                           3.24                            3.68 
[1] "1.4 - 18.4 (3.2)" "0.0 - 30.7 (3.7)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
"AMP PEAK 23(19P13.11) WILD-TYPE"   "AMP PEAK 23(19P13.11) MUTATED" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "AMP PEAK 23(19P13.11) MUTATED"   "AMP PEAK 23(19P13.11) MUTATED" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "AMP PEAK 23(19P13.11) MUTATED" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-LN-A4A9 
"AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
"AMP PEAK 23(19P13.11) WILD-TYPE"   "AMP PEAK 23(19P13.11) MUTATED" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "AMP PEAK 23(19P13.11) MUTATED"   "AMP PEAK 23(19P13.11) MUTATED" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "AMP PEAK 23(19P13.11) MUTATED" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-LN-A4A9 
"AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
"AMP PEAK 23(19P13.11) WILD-TYPE"   "AMP PEAK 23(19P13.11) MUTATED" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "AMP PEAK 23(19P13.11) MUTATED"   "AMP PEAK 23(19P13.11) MUTATED" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "AMP PEAK 23(19P13.11) MUTATED" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"AMP PEAK 23(19P13.11) WILD-TYPE" "AMP PEAK 23(19P13.11) WILD-TYPE" 
                     TCGA-LN-A4A9 
"AMP PEAK 23(19P13.11) WILD-TYPE" 
[1] "hr=" "3.8"
D22V2, continuous
                                 vv
clus                              STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 23(19P13.11) MUTATED          1         0         1          1
  AMP PEAK 23(19P13.11) WILD-TYPE        1         3         6          3
                                 vv
clus                              STAGE IIIB STAGE IIIC
  AMP PEAK 23(19P13.11) MUTATED            0          1
  AMP PEAK 23(19P13.11) WILD-TYPE          2          0
D22V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  AMP PEAK 23(19P13.11) MUTATED    2  1     1
  AMP PEAK 23(19P13.11) WILD-TYPE  2  6     7
D22V4, multiclass
       clus
vv      AMP PEAK 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE
  T1                                2                               2
  T2                                1                               6
  T3+T4                             1                               7
                                 vv
clus                              N0 N1+N2+N3
  AMP PEAK 23(19P13.11) MUTATED    1        3
  AMP PEAK 23(19P13.11) WILD-TYPE  6        9
D22V5, multiclass
          clus
vv         AMP PEAK 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE
  N0                                   1                               6
  N1+N2+N3                             3                               9
D22V6, binary
                                 cls
clus                               0  1
  AMP PEAK 23(19P13.11) MUTATED    0  4
  AMP PEAK 23(19P13.11) WILD-TYPE  3 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(19P13.11) MUTATED      0    4
  AMP PEAK 23(19P13.11) WILD-TYPE    3   12
        clus
vv       AMP PEAK 23(19P13.11) MUTATED AMP PEAK 23(19P13.11) WILD-TYPE
  FEMALE                             0                               3
  MALE                               4                              12
D22V7, continuous

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 5 2
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                           8                            7 
  AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE 
                           3                            2 
$`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-L5-A4OM TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        0.03         4.08        29.00         7.10         7.43         0.13 
TCGA-LN-A4A9 
        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                         4.08 
[1] "0.3 - 30.7 (3.4)" "0.0 - 29.0 (4.1)"
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-LN-A4A9 
"AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-LN-A4A9 
"AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"AMP PEAK 24(19Q12) WILD-TYPE"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
  "AMP PEAK 24(19Q12) MUTATED"   "AMP PEAK 24(19Q12) MUTATED" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"AMP PEAK 24(19Q12) WILD-TYPE" "AMP PEAK 24(19Q12) WILD-TYPE" 
                  TCGA-LN-A4A9 
"AMP PEAK 24(19Q12) WILD-TYPE" 
[1] "hr=" "1.2"
D23V2, continuous
                              vv
clus                           STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 24(19Q12) MUTATED          1         0         3          1
  AMP PEAK 24(19Q12) WILD-TYPE        1         3         4          3
                              vv
clus                           STAGE IIIB STAGE IIIC
  AMP PEAK 24(19Q12) MUTATED            2          1
  AMP PEAK 24(19Q12) WILD-TYPE          0          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     5
D23V4, multiclass
       clus
vv      AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  T1                             3                            1
  T2                             2                            5
  T3+T4                          3                            5
                              vv
clus                           N0 N1+N2+N3
  AMP PEAK 24(19Q12) MUTATED    1        7
  AMP PEAK 24(19Q12) WILD-TYPE  6        5
D23V5, multiclass
          clus
vv         AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  N0                                1                            6
  N1+N2+N3                          7                            5
D23V6, binary
                              cls
clus                           0 1
  AMP PEAK 24(19Q12) MUTATED   1 7
  AMP PEAK 24(19Q12) WILD-TYPE 2 9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(19Q12) MUTATED      1    7
  AMP PEAK 24(19Q12) WILD-TYPE    2    9
        clus
vv       AMP PEAK 24(19Q12) MUTATED AMP PEAK 24(19Q12) WILD-TYPE
  FEMALE                          1                            2
  MALE                            7                            9
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 9 2
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                            4                            11 
  AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE 
                            3                             2 
$`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-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         3.48         3.68         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 
        3.32        30.71        29.00         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                          3.68 
[1] "0.1 - 7.1 (2.3)"  "0.0 - 30.7 (3.7)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK 25(XP11.4) WILD-TYPE"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK 25(XP11.4) MUTATED" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK 25(XP11.4) WILD-TYPE"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK 25(XP11.4) WILD-TYPE"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK 25(XP11.4) MUTATED" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK 25(XP11.4) WILD-TYPE"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"AMP PEAK 25(XP11.4) WILD-TYPE"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "AMP PEAK 25(XP11.4) MUTATED" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"AMP PEAK 25(XP11.4) WILD-TYPE"   "AMP PEAK 25(XP11.4) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"AMP PEAK 25(XP11.4) WILD-TYPE" "AMP PEAK 25(XP11.4) WILD-TYPE" 
                   TCGA-LN-A4A9 
  "AMP PEAK 25(XP11.4) MUTATED" 
[1] "hr="     "6.2e+09"
D24V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  AMP PEAK 25(XP11.4) MUTATED          1         1         1          1
  AMP PEAK 25(XP11.4) WILD-TYPE        1         2         6          3
                               vv
clus                            STAGE IIIB STAGE IIIC
  AMP PEAK 25(XP11.4) MUTATED            0          0
  AMP PEAK 25(XP11.4) WILD-TYPE          2          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     8
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                             8
                               vv
clus                            N0 N1+N2+N3
  AMP PEAK 25(XP11.4) MUTATED    2        2
  AMP PEAK 25(XP11.4) WILD-TYPE  5       10
D24V5, multiclass
          clus
vv         AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE
  N0                                 2                             5
  N1+N2+N3                           2                            10
D24V6, binary
                               cls
clus                             0  1
  AMP PEAK 25(XP11.4) MUTATED    1  3
  AMP PEAK 25(XP11.4) WILD-TYPE  2 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XP11.4) MUTATED      1    3
  AMP PEAK 25(XP11.4) WILD-TYPE    2   13
        clus
vv       AMP PEAK 25(XP11.4) MUTATED AMP PEAK 25(XP11.4) WILD-TYPE
  FEMALE                           1                             2
  MALE                             3                            13
D24V7, continuous

Clustering(25) Variable = DEL PEAK  1(1P36.13) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                            0 1
  DEL PEAK  1(1P36.13) MUTATED   5 3
  DEL PEAK  1(1P36.13) WILD-TYPE 5 2
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                             8                              7 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                             3                              2 
$`DEL PEAK  1(1P36.13) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OR TCGA-L5-A4OU 
        0.03         0.26         3.48         3.68         3.16        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX 
        7.10         7.43 

$`DEL PEAK  1(1P36.13) WILD-TYPE`
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-LN-A4A2 
        4.08        18.35         3.32         1.38        30.71         0.13 
TCGA-LN-A4A9 
        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 
                          3.58                           3.32 
[1] "0.0 - 29.0 (3.6)" "0.1 - 30.7 (3.3)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-LN-A4A9 
"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-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-LN-A4A9 
"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-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK  1(1P36.13) WILD-TYPE" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK  1(1P36.13) MUTATED"   "DEL PEAK  1(1P36.13) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK  1(1P36.13) MUTATED" "DEL PEAK  1(1P36.13) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK  1(1P36.13) WILD-TYPE" 
[1] "hr=" "1.4"
D25V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK  1(1P36.13) MUTATED          1         1         4          0
  DEL PEAK  1(1P36.13) WILD-TYPE        1         2         3          4
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK  1(1P36.13) MUTATED            2          0
  DEL PEAK  1(1P36.13) WILD-TYPE          0          1
D25V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK  1(1P36.13) MUTATED    2  3     3
  DEL PEAK  1(1P36.13) WILD-TYPE  2  4     5
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                            3                              5
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK  1(1P36.13) MUTATED    2        6
  DEL PEAK  1(1P36.13) WILD-TYPE  5        6
D25V5, multiclass
          clus
vv         DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  N0                                  2                              5
  N1+N2+N3                            6                              6
D25V6, binary
                                cls
clus                             0 1
  DEL PEAK  1(1P36.13) MUTATED   1 7
  DEL PEAK  1(1P36.13) WILD-TYPE 2 9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED      1    7
  DEL PEAK  1(1P36.13) WILD-TYPE    2    9
        clus
vv       DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  FEMALE                            1                              2
  MALE                              7                              9
D25V7, continuous

Clustering(26) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  2(1P13.2) MUTATED   5 2
  DEL PEAK  2(1P13.2) WILD-TYPE 5 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            7                             8 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            2                             3 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        0.03         0.26         3.48        29.00         7.10         7.43 
TCGA-LN-A4A9 
        0.07 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        3.68         4.08        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-LN-A4A2 
       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 
                         3.48                          3.50 
[1] "0.0 - 29.0 (3.5)" "0.1 - 30.7 (3.5)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK  2(1P13.2) MUTATED" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  2(1P13.2) MUTATED" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK  2(1P13.2) MUTATED" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  2(1P13.2) MUTATED" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK  2(1P13.2) MUTATED" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  2(1P13.2) MUTATED" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-LN-A4A9 
  "DEL PEAK  2(1P13.2) MUTATED" 
[1] "hr=" "1.2"
D26V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK  2(1P13.2) MUTATED          0         2         3          1
  DEL PEAK  2(1P13.2) WILD-TYPE        2         1         4          3
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK  2(1P13.2) MUTATED            2          0
  DEL PEAK  2(1P13.2) WILD-TYPE          0          1
D26V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  2(1P13.2) MUTATED    0  4     4
  DEL PEAK  2(1P13.2) WILD-TYPE  4  3     4
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                           4                             4
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK  2(1P13.2) MUTATED    2        6
  DEL PEAK  2(1P13.2) WILD-TYPE  5        6
D26V5, multiclass
          clus
vv         DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                                 2                             5
  N1+N2+N3                           6                             6
D26V6, binary
                               cls
clus                            0 1
  DEL PEAK  2(1P13.2) MUTATED   1 7
  DEL PEAK  2(1P13.2) WILD-TYPE 2 9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      1    7
  DEL PEAK  2(1P13.2) WILD-TYPE    2    9
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                           1                             2
  MALE                             7                             9
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 7 5
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          3                          12 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          0                           5 
$`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-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.03         3.68         4.08        18.35         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       30.71        29.00         7.10         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                        3.88 
[1] "0.3 - 3.5 (3.3)"  "0.0 - 30.7 (3.9)"
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-L5-A4OE                  TCGA-L5-A4OF 
  "DEL PEAK  3(1Q44) MUTATED" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
  "DEL PEAK  3(1Q44) MUTATED" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OR                  TCGA-L5-A4OS 
"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-A4A2 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-LN-A4A9 
"DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-L5-A4OE                  TCGA-L5-A4OF 
  "DEL PEAK  3(1Q44) MUTATED" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
  "DEL PEAK  3(1Q44) MUTATED" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OR                  TCGA-L5-A4OS 
"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-A4A2 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-LN-A4A9 
"DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
"DEL PEAK  3(1Q44) WILD-TYPE"   "DEL PEAK  3(1Q44) MUTATED" 
                 TCGA-L5-A4OE                  TCGA-L5-A4OF 
  "DEL PEAK  3(1Q44) MUTATED" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
  "DEL PEAK  3(1Q44) MUTATED" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-L5-A4OR                  TCGA-L5-A4OS 
"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-A4A2 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-LN-A4A9 
"DEL PEAK  3(1Q44) WILD-TYPE" 
[1] "hr="     "2.5e+08"
D27V2, continuous
                             vv
clus                          STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK  3(1Q44) MUTATED          0         0         0          0
  DEL PEAK  3(1Q44) WILD-TYPE        2         3         7          4
                             vv
clus                          STAGE IIIB STAGE IIIC
  DEL PEAK  3(1Q44) MUTATED            2          1
  DEL PEAK  3(1Q44) WILD-TYPE          0          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     5
D27V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T1                            0                           4
  T2                            0                           7
  T3+T4                         3                           5
                             vv
clus                          N0 N1+N2+N3
  DEL PEAK  3(1Q44) MUTATED    0        3
  DEL PEAK  3(1Q44) WILD-TYPE  7        9
D27V5, multiclass
          clus
vv         DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                               0                           7
  N1+N2+N3                         3                           9
D27V6, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q44) MUTATED    0  3
  DEL PEAK  3(1Q44) WILD-TYPE  3 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0    3
  DEL PEAK  3(1Q44) WILD-TYPE    3   13
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                         0                           3
  MALE                           3                          13
D27V7, continuous
[1] "Remove cluster labels:"    "DEL PEAK  3(1Q44) MUTATED"
clus
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          2                          10 
                 TCGA-IG-A3Y9                  TCGA-IG-A3YA 
"DEL PEAK  3(1Q44) WILD-TYPE" "DEL PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-IG-A4P3                  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   3 1
  DEL PEAK  4(2Q22.1) WILD-TYPE 7 4
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            4                            11 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            1                             4 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OS TCGA-L5-A4OX 
        0.03         3.48        30.71         7.43 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.68         4.08        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A2 TCGA-LN-A4A9 
        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 
                        5.455                         3.320 
[1] "0.0 - 30.7 (5.5)" "0.1 - 29.0 (3.3)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  4(2Q22.1) WILD-TYPE"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  4(2Q22.1) WILD-TYPE"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  4(2Q22.1) WILD-TYPE"   "DEL PEAK  4(2Q22.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  4(2Q22.1) WILD-TYPE" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  4(2Q22.1) MUTATED" "DEL PEAK  4(2Q22.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"DEL PEAK  4(2Q22.1) WILD-TYPE" 
[1] "hr=" "2.3"
D28V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK  4(2Q22.1) MUTATED          0         0         4          2
  DEL PEAK  4(2Q22.1) WILD-TYPE        2         3         3          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK  4(2Q22.1) MUTATED            1          0
  DEL PEAK  4(2Q22.1) WILD-TYPE          1          1
D28V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  4(2Q22.1) MUTATED    0  4     3
  DEL PEAK  4(2Q22.1) WILD-TYPE  4  3     5
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                           3                             5
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK  4(2Q22.1) MUTATED    1        6
  DEL PEAK  4(2Q22.1) WILD-TYPE  6        6
D28V5, multiclass
          clus
vv         DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                                 1                             6
  N1+N2+N3                           6                             6
D28V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED    1  6
  DEL PEAK  4(2Q22.1) WILD-TYPE  2 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      1    6
  DEL PEAK  4(2Q22.1) WILD-TYPE    2   10
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                           1                             2
  MALE                             6                            10
D28V7, continuous

Clustering(29) Variable = DEL PEAK  5(2Q34) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                         0 1
  DEL PEAK  5(2Q34) MUTATED   3 1
  DEL PEAK  5(2Q34) WILD-TYPE 7 4
  DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE 
                          4                          11 
  DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE 
                          1                           4 
$`DEL PEAK  5(2Q34) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OS TCGA-L5-A4OW TCGA-LN-A4A9 
        0.03        30.71         7.10         0.07 

$`DEL PEAK  5(2Q34) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.48         3.68         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38         3.16        29.00         7.43         0.13 

  DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE 
                       0.03                        0.13 
  DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE 
                      30.71                       29.00 
  DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE 
                      3.585                       3.480 
[1] "0.0 - 30.7 (3.6)" "0.1 - 29.0 (3.5)"
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
  "DEL PEAK  5(2Q34) MUTATED" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OE                  TCGA-L5-A4OF 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OR                  TCGA-L5-A4OS 
"DEL PEAK  5(2Q34) WILD-TYPE"   "DEL PEAK  5(2Q34) MUTATED" 
                 TCGA-L5-A4OU                  TCGA-L5-A4OW 
"DEL PEAK  5(2Q34) WILD-TYPE"   "DEL PEAK  5(2Q34) MUTATED" 
                 TCGA-L5-A4OX                  TCGA-LN-A4A2 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-LN-A4A9 
  "DEL PEAK  5(2Q34) MUTATED" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
  "DEL PEAK  5(2Q34) MUTATED" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OE                  TCGA-L5-A4OF 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OR                  TCGA-L5-A4OS 
"DEL PEAK  5(2Q34) WILD-TYPE"   "DEL PEAK  5(2Q34) MUTATED" 
                 TCGA-L5-A4OU                  TCGA-L5-A4OW 
"DEL PEAK  5(2Q34) WILD-TYPE"   "DEL PEAK  5(2Q34) MUTATED" 
                 TCGA-L5-A4OX                  TCGA-LN-A4A2 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-LN-A4A9 
  "DEL PEAK  5(2Q34) MUTATED" 
                 TCGA-IG-A4P3                  TCGA-IG-A4QS 
  "DEL PEAK  5(2Q34) MUTATED" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OE                  TCGA-L5-A4OF 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OM                  TCGA-L5-A4ON 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OO                  TCGA-L5-A4OQ 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-L5-A4OR                  TCGA-L5-A4OS 
"DEL PEAK  5(2Q34) WILD-TYPE"   "DEL PEAK  5(2Q34) MUTATED" 
                 TCGA-L5-A4OU                  TCGA-L5-A4OW 
"DEL PEAK  5(2Q34) WILD-TYPE"   "DEL PEAK  5(2Q34) MUTATED" 
                 TCGA-L5-A4OX                  TCGA-LN-A4A2 
"DEL PEAK  5(2Q34) WILD-TYPE" "DEL PEAK  5(2Q34) WILD-TYPE" 
                 TCGA-LN-A4A9 
  "DEL PEAK  5(2Q34) MUTATED" 
[1] "hr=" "1.5"
D29V2, continuous
                             vv
clus                          STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK  5(2Q34) MUTATED          0         1         3          2
  DEL PEAK  5(2Q34) WILD-TYPE        2         2         4          2
                             vv
clus                          STAGE IIIB STAGE IIIC
  DEL PEAK  5(2Q34) MUTATED            0          0
  DEL PEAK  5(2Q34) WILD-TYPE          2          1
D29V3, multiclass
                             vv
clus                          T1 T2 T3+T4
  DEL PEAK  5(2Q34) MUTATED    0  4     2
  DEL PEAK  5(2Q34) WILD-TYPE  4  3     6
D29V4, multiclass
       clus
vv      DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE
  T1                            0                           4
  T2                            4                           3
  T3+T4                         2                           6
                             vv
clus                          N0 N1+N2+N3
  DEL PEAK  5(2Q34) MUTATED    2        4
  DEL PEAK  5(2Q34) WILD-TYPE  5        8
D29V5, multiclass
          clus
vv         DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE
  N0                               2                           5
  N1+N2+N3                         4                           8
D29V6, binary
                             cls
clus                           0  1
  DEL PEAK  5(2Q34) MUTATED    2  4
  DEL PEAK  5(2Q34) WILD-TYPE  1 12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2Q34) MUTATED      2    4
  DEL PEAK  5(2Q34) WILD-TYPE    1   12
        clus
vv       DEL PEAK  5(2Q34) MUTATED DEL PEAK  5(2Q34) WILD-TYPE
  FEMALE                         2                           1
  MALE                           4                          12
D29V7, continuous

Clustering(30) Variable = DEL PEAK  6(3P26.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  6(3P26.1) MUTATED   5 2
  DEL PEAK  6(3P26.1) WILD-TYPE 5 3
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                            7                             8 
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                            2                             3 
$`DEL PEAK  6(3P26.1) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        0.26         4.08         3.32         3.16        30.71         7.10 
TCGA-LN-A4A2 
        0.13 

$`DEL PEAK  6(3P26.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU 
        0.03         3.48         3.68        18.35         1.38        29.00 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                        30.71                         29.00 
  DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE 
                         3.32                          3.58 
[1] "0.1 - 30.7 (3.3)" "0.0 - 29.0 (3.6)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK  6(3P26.1) WILD-TYPE"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK  6(3P26.1) WILD-TYPE" "DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK  6(3P26.1) MUTATED" "DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK  6(3P26.1) MUTATED" "DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK  6(3P26.1) MUTATED"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  6(3P26.1) WILD-TYPE"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK  6(3P26.1) WILD-TYPE"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK  6(3P26.1) WILD-TYPE"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK  6(3P26.1) WILD-TYPE" "DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK  6(3P26.1) MUTATED" "DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK  6(3P26.1) MUTATED" "DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK  6(3P26.1) MUTATED"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  6(3P26.1) WILD-TYPE"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK  6(3P26.1) WILD-TYPE"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK  6(3P26.1) WILD-TYPE"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK  6(3P26.1) WILD-TYPE" "DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK  6(3P26.1) MUTATED" "DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK  6(3P26.1) MUTATED" "DEL PEAK  6(3P26.1) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK  6(3P26.1) MUTATED"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  6(3P26.1) WILD-TYPE"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK  6(3P26.1) WILD-TYPE"   "DEL PEAK  6(3P26.1) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK  6(3P26.1) WILD-TYPE" 
[1] "hr=" "1.1"
D30V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK  6(3P26.1) MUTATED          2         1         3          3
  DEL PEAK  6(3P26.1) WILD-TYPE        0         2         4          1
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK  6(3P26.1) MUTATED            1          1
  DEL PEAK  6(3P26.1) WILD-TYPE          1          0
D30V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  6(3P26.1) MUTATED    2  3     6
  DEL PEAK  6(3P26.1) WILD-TYPE  2  4     2
D30V4, multiclass
       clus
vv      DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  T1                              2                             2
  T2                              3                             4
  T3+T4                           6                             2
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK  6(3P26.1) MUTATED    5        6
  DEL PEAK  6(3P26.1) WILD-TYPE  2        6
D30V5, multiclass
          clus
vv         DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  N0                                 5                             2
  N1+N2+N3                           6                             6
D30V6, binary
                               cls
clus                            0 1
  DEL PEAK  6(3P26.1) MUTATED   3 8
  DEL PEAK  6(3P26.1) WILD-TYPE 0 8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.1) MUTATED      3    8
  DEL PEAK  6(3P26.1) WILD-TYPE    0    8
        clus
vv       DEL PEAK  6(3P26.1) MUTATED DEL PEAK  6(3P26.1) WILD-TYPE
  FEMALE                           3                             0
  MALE                             8                             8
D30V7, continuous

Clustering(31) Variable = DEL PEAK  7(3P14.3) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  7(3P14.3) MUTATED   6 3
  DEL PEAK  7(3P14.3) WILD-TYPE 4 2
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                            9                             6 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                            3                             2 
$`DEL PEAK  7(3P14.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.03         0.26         3.68         4.08         3.32         1.38 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        7.10         7.43         0.13 

$`DEL PEAK  7(3P14.3) WILD-TYPE`
TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-LN-A4A9 
        3.48        18.35         3.16        30.71        29.00         0.07 

  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                         7.43                         30.71 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                        3.320                        10.915 
[1] "0.0 - 7.4 (3.3)"   "0.1 - 30.7 (10.9)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  7(3P14.3) MUTATED"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK  7(3P14.3) WILD-TYPE"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK  7(3P14.3) MUTATED" "DEL PEAK  7(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK  7(3P14.3) MUTATED"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  7(3P14.3) WILD-TYPE" "DEL PEAK  7(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  7(3P14.3) WILD-TYPE"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  7(3P14.3) MUTATED"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK  7(3P14.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  7(3P14.3) MUTATED"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK  7(3P14.3) WILD-TYPE"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK  7(3P14.3) MUTATED" "DEL PEAK  7(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK  7(3P14.3) MUTATED"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  7(3P14.3) WILD-TYPE" "DEL PEAK  7(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  7(3P14.3) WILD-TYPE"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  7(3P14.3) MUTATED"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK  7(3P14.3) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  7(3P14.3) MUTATED"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK  7(3P14.3) WILD-TYPE"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK  7(3P14.3) MUTATED" "DEL PEAK  7(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK  7(3P14.3) MUTATED"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  7(3P14.3) WILD-TYPE" "DEL PEAK  7(3P14.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  7(3P14.3) WILD-TYPE"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  7(3P14.3) MUTATED"   "DEL PEAK  7(3P14.3) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK  7(3P14.3) WILD-TYPE" 
[1] "hr=" "4.4"
D31V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK  7(3P14.3) MUTATED          1         1         5          4
  DEL PEAK  7(3P14.3) WILD-TYPE        1         2         2          0
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK  7(3P14.3) MUTATED            1          1
  DEL PEAK  7(3P14.3) WILD-TYPE          1          0
D31V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  7(3P14.3) MUTATED    2  5     6
  DEL PEAK  7(3P14.3) WILD-TYPE  2  2     2
D31V4, multiclass
       clus
vv      DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  T1                              2                             2
  T2                              5                             2
  T3+T4                           6                             2
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK  7(3P14.3) MUTATED    4        9
  DEL PEAK  7(3P14.3) WILD-TYPE  3        3
D31V5, multiclass
          clus
vv         DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  N0                                 4                             3
  N1+N2+N3                           9                             3
D31V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED    2 11
  DEL PEAK  7(3P14.3) WILD-TYPE  1  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED      2   11
  DEL PEAK  7(3P14.3) WILD-TYPE    1    5
        clus
vv       DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  FEMALE                           2                             1
  MALE                            11                             5
D31V7, continuous

Clustering(32) Variable = DEL PEAK  8(3P14.2) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  8(3P14.2) MUTATED   7 3
  DEL PEAK  8(3P14.2) WILD-TYPE 3 2
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           10                             5 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                            3                             2 
$`DEL PEAK  8(3P14.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO 
        0.03         0.26         3.48         3.68         4.08         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38         7.10         7.43         0.13 

$`DEL PEAK  8(3P14.2) WILD-TYPE`
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-LN-A4A9 
       18.35         3.16        30.71        29.00         0.07 

  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         7.43                         30.71 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         3.40                         18.35 
[1] "0.0 - 7.4 (3.4)"   "0.1 - 30.7 (18.4)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK  8(3P14.2) MUTATED" "DEL PEAK  8(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  8(3P14.2) WILD-TYPE" "DEL PEAK  8(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  8(3P14.2) WILD-TYPE"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK  8(3P14.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK  8(3P14.2) MUTATED" "DEL PEAK  8(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  8(3P14.2) WILD-TYPE" "DEL PEAK  8(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  8(3P14.2) WILD-TYPE"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK  8(3P14.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK  8(3P14.2) MUTATED" "DEL PEAK  8(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK  8(3P14.2) WILD-TYPE" "DEL PEAK  8(3P14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK  8(3P14.2) WILD-TYPE"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK  8(3P14.2) MUTATED"   "DEL PEAK  8(3P14.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK  8(3P14.2) WILD-TYPE" 
[1] "hr=" "3.8"
D32V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK  8(3P14.2) MUTATED          1         1         5          4
  DEL PEAK  8(3P14.2) WILD-TYPE        1         2         2          0
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK  8(3P14.2) MUTATED            2          1
  DEL PEAK  8(3P14.2) WILD-TYPE          0          0
D32V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK  8(3P14.2) MUTATED    2  5     7
  DEL PEAK  8(3P14.2) WILD-TYPE  2  2     1
D32V4, multiclass
       clus
vv      DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T1                              2                             2
  T2                              5                             2
  T3+T4                           7                             1
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK  8(3P14.2) MUTATED    4       10
  DEL PEAK  8(3P14.2) WILD-TYPE  3        2
D32V5, multiclass
          clus
vv         DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                                 4                             3
  N1+N2+N3                          10                             2
D32V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED    2 12
  DEL PEAK  8(3P14.2) WILD-TYPE  1  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED      2   12
  DEL PEAK  8(3P14.2) WILD-TYPE    1    4
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                           2                             1
  MALE                            12                             4
D32V7, continuous

Clustering(33) Variable = DEL PEAK 10(3Q26.31) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(3Q26.31) MUTATED    0  3
  DEL PEAK 10(3Q26.31) WILD-TYPE 10  2
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             3                             12 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                             3                              2 
$`DEL PEAK 10(3Q26.31) MUTATED`
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OX 
       18.35         1.38         7.43 

$`DEL PEAK 10(3Q26.31) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO 
        0.03         0.26         3.48         3.68         4.08         3.32 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.16        30.71        29.00         7.10         0.13         0.07 

  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          1.38                           0.03 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                         18.35                          30.71 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          7.43                           3.40 
[1] "1.4 - 18.4 (7.4)" "0.0 - 30.7 (3.4)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 10(3Q26.31) WILD-TYPE"   "DEL PEAK 10(3Q26.31) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 10(3Q26.31) WILD-TYPE"   "DEL PEAK 10(3Q26.31) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 10(3Q26.31) MUTATED" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 10(3Q26.31) WILD-TYPE"   "DEL PEAK 10(3Q26.31) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 10(3Q26.31) WILD-TYPE"   "DEL PEAK 10(3Q26.31) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 10(3Q26.31) MUTATED" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 10(3Q26.31) WILD-TYPE"   "DEL PEAK 10(3Q26.31) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 10(3Q26.31) WILD-TYPE"   "DEL PEAK 10(3Q26.31) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 10(3Q26.31) WILD-TYPE" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 10(3Q26.31) MUTATED" "DEL PEAK 10(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 10(3Q26.31) WILD-TYPE" 
[1] "hr=" "3.1"
D33V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 10(3Q26.31) MUTATED          0         0         2          1
  DEL PEAK 10(3Q26.31) WILD-TYPE        2         3         5          3
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 10(3Q26.31) MUTATED            0          0
  DEL PEAK 10(3Q26.31) WILD-TYPE          2          1
D33V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 10(3Q26.31) MUTATED    1  2     0
  DEL PEAK 10(3Q26.31) WILD-TYPE  3  5     8
D33V4, multiclass
       clus
vv      DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  T1                               1                              3
  T2                               2                              5
  T3+T4                            0                              8
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 10(3Q26.31) MUTATED    0        3
  DEL PEAK 10(3Q26.31) WILD-TYPE  7        9
D33V5, multiclass
          clus
vv         DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  N0                                  0                              7
  N1+N2+N3                            3                              9
D33V6, binary
                                cls
clus                              0  1
  DEL PEAK 10(3Q26.31) MUTATED    0  3
  DEL PEAK 10(3Q26.31) WILD-TYPE  3 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      0    3
  DEL PEAK 10(3Q26.31) WILD-TYPE    3   13
        clus
vv       DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  FEMALE                            0                              3
  MALE                              3                             13
D33V7, continuous

Clustering(34) Variable = DEL PEAK 11(4P15.2) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 11(4P15.2) MUTATED   6 3
  DEL PEAK 11(4P15.2) WILD-TYPE 4 2
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                            9                             6 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                            3                             2 
$`DEL PEAK 11(4P15.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         0.26         3.48         4.08         3.32         3.16 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        7.10         7.43         0.13 

$`DEL PEAK 11(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 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                         7.43                         30.71 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                        3.320                        11.015 
[1] "0.0 - 7.4 (3.3)"   "0.1 - 30.7 (11.0)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 11(4P15.2) MUTATED"   "DEL PEAK 11(4P15.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 11(4P15.2) WILD-TYPE"   "DEL PEAK 11(4P15.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK 11(4P15.2) MUTATED"   "DEL PEAK 11(4P15.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 11(4P15.2) MUTATED"   "DEL PEAK 11(4P15.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 11(4P15.2) WILD-TYPE"   "DEL PEAK 11(4P15.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK 11(4P15.2) MUTATED"   "DEL PEAK 11(4P15.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 11(4P15.2) MUTATED"   "DEL PEAK 11(4P15.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 11(4P15.2) MUTATED" "DEL PEAK 11(4P15.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 11(4P15.2) WILD-TYPE"   "DEL PEAK 11(4P15.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK 11(4P15.2) MUTATED"   "DEL PEAK 11(4P15.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 11(4P15.2) WILD-TYPE" 
[1] "hr=" "4.1"
D34V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 11(4P15.2) MUTATED          2         1         3          2
  DEL PEAK 11(4P15.2) WILD-TYPE        0         2         4          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 11(4P15.2) MUTATED            2          1
  DEL PEAK 11(4P15.2) WILD-TYPE          0          0
D34V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 11(4P15.2) MUTATED    2  3     6
  DEL PEAK 11(4P15.2) WILD-TYPE  2  4     2
D34V4, multiclass
       clus
vv      DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T1                              2                             2
  T2                              3                             4
  T3+T4                           6                             2
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 11(4P15.2) MUTATED    5        6
  DEL PEAK 11(4P15.2) WILD-TYPE  2        6
D34V5, multiclass
          clus
vv         DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                                 5                             2
  N1+N2+N3                           6                             6
D34V6, binary
                               cls
clus                            0 1
  DEL PEAK 11(4P15.2) MUTATED   2 9
  DEL PEAK 11(4P15.2) WILD-TYPE 1 7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED      2    9
  DEL PEAK 11(4P15.2) WILD-TYPE    1    7
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                           2                             1
  MALE                             9                             7
D34V7, continuous

Clustering(35) Variable = DEL PEAK 12(4Q22.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 12(4Q22.1) MUTATED   4 4
  DEL PEAK 12(4Q22.1) WILD-TYPE 6 1
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                            8                             7 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                            4                             1 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        0.26         3.48         3.32         1.38         3.16        30.71 
TCGA-L5-A4OW TCGA-L5-A4OX 
        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 
                         3.40                          3.68 
[1] "0.3 - 30.7 (3.4)" "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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 12(4Q22.1) MUTATED" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 12(4Q22.1) WILD-TYPE" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 12(4Q22.1) WILD-TYPE"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK 12(4Q22.1) MUTATED" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 12(4Q22.1) MUTATED" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 12(4Q22.1) WILD-TYPE" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 12(4Q22.1) WILD-TYPE"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK 12(4Q22.1) MUTATED" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 12(4Q22.1) MUTATED" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 12(4Q22.1) WILD-TYPE" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 12(4Q22.1) MUTATED"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 12(4Q22.1) WILD-TYPE"   "DEL PEAK 12(4Q22.1) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK 12(4Q22.1) MUTATED" "DEL PEAK 12(4Q22.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"DEL PEAK 12(4Q22.1) WILD-TYPE" 
[1] "hr=" "3.7"
D35V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 12(4Q22.1) MUTATED          1         0         3          2
  DEL PEAK 12(4Q22.1) WILD-TYPE        1         3         4          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 12(4Q22.1) MUTATED            2          1
  DEL PEAK 12(4Q22.1) WILD-TYPE          0          0
D35V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 12(4Q22.1) MUTATED    1  4     4
  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                           4                             4
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 12(4Q22.1) MUTATED    2        7
  DEL PEAK 12(4Q22.1) WILD-TYPE  5        5
D35V5, multiclass
          clus
vv         DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                                 2                             5
  N1+N2+N3                           7                             5
D35V6, binary
                               cls
clus                            0 1
  DEL PEAK 12(4Q22.1) MUTATED   2 7
  DEL PEAK 12(4Q22.1) WILD-TYPE 1 9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      2    7
  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                             7                             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   7 2
  DEL PEAK 13(5Q11.2) WILD-TYPE 3 3
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                            9                             6 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                            2                             3 
$`DEL PEAK 13(5Q11.2) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR 
        0.26         3.48         3.68         4.08         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-LN-A4A2 
       30.71         7.10         0.13 

$`DEL PEAK 13(5Q11.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A9 
        0.03        18.35         1.38        29.00         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 
                        3.480                         4.405 
[1] "0.1 - 30.7 (3.5)" "0.0 - 29.0 (4.4)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 13(5Q11.2) MUTATED"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 13(5Q11.2) MUTATED"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 13(5Q11.2) MUTATED"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 13(5Q11.2) MUTATED"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 13(5Q11.2) MUTATED"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 13(5Q11.2) MUTATED" "DEL PEAK 13(5Q11.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 13(5Q11.2) MUTATED"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 13(5Q11.2) WILD-TYPE"   "DEL PEAK 13(5Q11.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 13(5Q11.2) WILD-TYPE" 
[1] "hr=" "1.3"
D36V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 13(5Q11.2) MUTATED          2         1         4          2
  DEL PEAK 13(5Q11.2) WILD-TYPE        0         2         3          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 13(5Q11.2) MUTATED            2          1
  DEL PEAK 13(5Q11.2) WILD-TYPE          0          0
D36V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 13(5Q11.2) MUTATED    3  3     6
  DEL PEAK 13(5Q11.2) WILD-TYPE  1  4     2
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                           6                             2
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 13(5Q11.2) MUTATED    4        8
  DEL PEAK 13(5Q11.2) WILD-TYPE  3        4
D36V5, multiclass
          clus
vv         DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  N0                                 4                             3
  N1+N2+N3                           8                             4
D36V6, binary
                               cls
clus                            0 1
  DEL PEAK 13(5Q11.2) MUTATED   3 9
  DEL PEAK 13(5Q11.2) WILD-TYPE 0 7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED      3    9
  DEL PEAK 13(5Q11.2) WILD-TYPE    0    7
        clus
vv       DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  FEMALE                           3                             0
  MALE                             9                             7
D36V7, continuous

Clustering(37) Variable = DEL PEAK 14(5Q12.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 14(5Q12.3) MUTATED   7 2
  DEL PEAK 14(5Q12.3) WILD-TYPE 3 3
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                            9                             6 
  DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE 
                            2                             3 
$`DEL PEAK 14(5Q12.3) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR 
        0.26         3.48         3.68         4.08         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-LN-A4A2 
       30.71         7.10         0.13 

$`DEL PEAK 14(5Q12.3) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A9 
        0.03        18.35         1.38        29.00         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 
                        3.480                         4.405 
[1] "0.1 - 30.7 (3.5)" "0.0 - 29.0 (4.4)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 14(5Q12.3) MUTATED"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 14(5Q12.3) MUTATED"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 14(5Q12.3) MUTATED"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 14(5Q12.3) MUTATED"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 14(5Q12.3) MUTATED"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 14(5Q12.3) MUTATED" "DEL PEAK 14(5Q12.3) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 14(5Q12.3) MUTATED"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 14(5Q12.3) WILD-TYPE"   "DEL PEAK 14(5Q12.3) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 14(5Q12.3) WILD-TYPE" 
[1] "hr=" "1.3"
D37V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 14(5Q12.3) MUTATED          2         1         4          2
  DEL PEAK 14(5Q12.3) WILD-TYPE        0         2         3          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 14(5Q12.3) MUTATED            2          1
  DEL PEAK 14(5Q12.3) WILD-TYPE          0          0
D37V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 14(5Q12.3) MUTATED    3  3     6
  DEL PEAK 14(5Q12.3) WILD-TYPE  1  4     2
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                           6                             2
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 14(5Q12.3) MUTATED    4        8
  DEL PEAK 14(5Q12.3) WILD-TYPE  3        4
D37V5, multiclass
          clus
vv         DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE
  N0                                 4                             3
  N1+N2+N3                           8                             4
D37V6, binary
                               cls
clus                            0 1
  DEL PEAK 14(5Q12.3) MUTATED   3 9
  DEL PEAK 14(5Q12.3) WILD-TYPE 0 7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.3) MUTATED      3    9
  DEL PEAK 14(5Q12.3) WILD-TYPE    0    7
        clus
vv       DEL PEAK 14(5Q12.3) MUTATED DEL PEAK 14(5Q12.3) WILD-TYPE
  FEMALE                           3                             0
  MALE                             9                             7
D37V7, continuous

Clustering(38) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 15(6P25.3) MUTATED   4 4
  DEL PEAK 15(6P25.3) WILD-TYPE 6 1
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                            8                             7 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                            4                             1 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.03         0.26        18.35         3.32         1.38         3.16 
TCGA-L5-A4OW TCGA-LN-A4A2 
        7.10         0.13 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX 
        3.48         3.68         4.08        30.71        29.00         7.43 
TCGA-LN-A4A9 
        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 
                         2.27                          4.08 
[1] "0.0 - 18.4 (2.3)" "0.1 - 30.7 (4.1)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 15(6P25.3) WILD-TYPE"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 15(6P25.3) WILD-TYPE"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 15(6P25.3) WILD-TYPE"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 15(6P25.3) WILD-TYPE"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 15(6P25.3) WILD-TYPE"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 15(6P25.3) WILD-TYPE"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 15(6P25.3) WILD-TYPE" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 15(6P25.3) WILD-TYPE"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 15(6P25.3) MUTATED"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 15(6P25.3) MUTATED" "DEL PEAK 15(6P25.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 15(6P25.3) WILD-TYPE"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 15(6P25.3) WILD-TYPE"   "DEL PEAK 15(6P25.3) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 15(6P25.3) WILD-TYPE" 
[1] "hr=" "7.2"
D38V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 15(6P25.3) MUTATED          1         1         3          1
  DEL PEAK 15(6P25.3) WILD-TYPE        1         2         4          3
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 15(6P25.3) MUTATED            1          1
  DEL PEAK 15(6P25.3) WILD-TYPE          1          0
D38V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 15(6P25.3) MUTATED    2  3     3
  DEL PEAK 15(6P25.3) WILD-TYPE  2  4     5
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                           3                             5
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 15(6P25.3) MUTATED    2        6
  DEL PEAK 15(6P25.3) WILD-TYPE  5        6
D38V5, multiclass
          clus
vv         DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                                 2                             5
  N1+N2+N3                           6                             6
D38V6, binary
                               cls
clus                            0 1
  DEL PEAK 15(6P25.3) MUTATED   1 7
  DEL PEAK 15(6P25.3) WILD-TYPE 2 9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      1    7
  DEL PEAK 15(6P25.3) WILD-TYPE    2    9
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                           1                             2
  MALE                             7                             9
D38V7, continuous

Clustering(39) Variable = DEL PEAK 16(6Q14.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 16(6Q14.2) MUTATED   2 1
  DEL PEAK 16(6Q14.2) WILD-TYPE 8 4
  DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE 
                            3                            12 
  DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE 
                            1                             4 
$`DEL PEAK 16(6Q14.2) MUTATED`
TCGA-L5-A4OR TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.16         0.13         0.07 

$`DEL PEAK 16(6Q14.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         3.48         3.68         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         1.38        30.71        29.00         7.10         7.43 

  DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE 
                         3.16                         30.71 
  DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE 
                         0.13                          3.88 
[1] "0.1 - 3.2 (0.1)"  "0.0 - 30.7 (3.9)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 16(6Q14.2) MUTATED" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 16(6Q14.2) WILD-TYPE"   "DEL PEAK 16(6Q14.2) MUTATED" 
                   TCGA-LN-A4A9 
  "DEL PEAK 16(6Q14.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 16(6Q14.2) MUTATED" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 16(6Q14.2) WILD-TYPE"   "DEL PEAK 16(6Q14.2) MUTATED" 
                   TCGA-LN-A4A9 
  "DEL PEAK 16(6Q14.2) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 16(6Q14.2) MUTATED" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 16(6Q14.2) WILD-TYPE"   "DEL PEAK 16(6Q14.2) MUTATED" 
                   TCGA-LN-A4A9 
  "DEL PEAK 16(6Q14.2) MUTATED" 
[1] "hr=" "9.5"
D39V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 16(6Q14.2) MUTATED          1         2         0          0
  DEL PEAK 16(6Q14.2) WILD-TYPE        1         1         7          4
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 16(6Q14.2) MUTATED            0          0
  DEL PEAK 16(6Q14.2) WILD-TYPE          2          1
D39V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 16(6Q14.2) MUTATED    1  1     1
  DEL PEAK 16(6Q14.2) WILD-TYPE  3  6     7
D39V4, multiclass
       clus
vv      DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE
  T1                              1                             3
  T2                              1                             6
  T3+T4                           1                             7
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 16(6Q14.2) MUTATED    3        0
  DEL PEAK 16(6Q14.2) WILD-TYPE  4       12
D39V5, multiclass
          clus
vv         DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE
  N0                                 3                             4
  N1+N2+N3                           0                            12
D39V6, binary
                               cls
clus                             0  1
  DEL PEAK 16(6Q14.2) MUTATED    0  3
  DEL PEAK 16(6Q14.2) WILD-TYPE  3 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q14.2) MUTATED      0    3
  DEL PEAK 16(6Q14.2) WILD-TYPE    3   13
        clus
vv       DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE
  FEMALE                           0                             3
  MALE                             3                            13
D39V7, continuous
[1] "Remove cluster labels:"      "DEL PEAK 16(6Q14.2) MUTATED"
clus
  DEL PEAK 16(6Q14.2) MUTATED DEL PEAK 16(6Q14.2) WILD-TYPE 
                            1                            11 
                   TCGA-IG-A3Y9                    TCGA-IG-A3YA 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-L5-A4OE 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 16(6Q14.2) WILD-TYPE" "DEL PEAK 16(6Q14.2) WILD-TYPE" 
                   TCGA-L5-A4OX 
"DEL PEAK 16(6Q14.2) 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 1
  DEL PEAK 17(7Q31.1) WILD-TYPE 6 4
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            5                            10 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            1                             4 
$`DEL PEAK 17(7Q31.1) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
        0.26         3.68         4.08         3.16        29.00 

$`DEL PEAK 17(7Q31.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.03         3.48        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 

  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 
                         3.68                          3.40 
[1] "0.3 - 29.0 (3.7)" "0.0 - 30.7 (3.4)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 17(7Q31.1) MUTATED" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 17(7Q31.1) MUTATED" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "DEL PEAK 17(7Q31.1) MUTATED" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 17(7Q31.1) MUTATED" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 17(7Q31.1) MUTATED" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "DEL PEAK 17(7Q31.1) MUTATED" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 17(7Q31.1) WILD-TYPE"   "DEL PEAK 17(7Q31.1) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 17(7Q31.1) MUTATED" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 17(7Q31.1) MUTATED" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "DEL PEAK 17(7Q31.1) MUTATED" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 17(7Q31.1) WILD-TYPE" "DEL PEAK 17(7Q31.1) WILD-TYPE" 
                   TCGA-LN-A4A9 
"DEL PEAK 17(7Q31.1) WILD-TYPE" 
[1] "hr=" "1.8"
D40V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 17(7Q31.1) MUTATED          2         1         2          2
  DEL PEAK 17(7Q31.1) WILD-TYPE        0         2         5          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 17(7Q31.1) MUTATED            1          0
  DEL PEAK 17(7Q31.1) WILD-TYPE          1          1
D40V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 17(7Q31.1) MUTATED    3  1     4
  DEL PEAK 17(7Q31.1) WILD-TYPE  1  6     4
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                           4                             4
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 17(7Q31.1) MUTATED    4        4
  DEL PEAK 17(7Q31.1) WILD-TYPE  3        8
D40V5, multiclass
          clus
vv         DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  N0                                 4                             3
  N1+N2+N3                           4                             8
D40V6, binary
                               cls
clus                            0 1
  DEL PEAK 17(7Q31.1) MUTATED   1 7
  DEL PEAK 17(7Q31.1) WILD-TYPE 2 9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      1    7
  DEL PEAK 17(7Q31.1) WILD-TYPE    2    9
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  FEMALE                           1                             2
  MALE                             7                             9
D40V7, continuous

Clustering(41) Variable = DEL PEAK 18(7Q36.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 18(7Q36.2) MUTATED   5 2
  DEL PEAK 18(7Q36.2) WILD-TYPE 5 3
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                            7                             8 
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                            2                             3 
$`DEL PEAK 18(7Q36.2) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS 
        0.03         3.68         4.08        18.35         3.16        30.71 
TCGA-L5-A4OU 
       29.00 

$`DEL PEAK 18(7Q36.2) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX 
        0.26         3.48         3.32         1.38         7.10         7.43 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        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 
                        30.71                          7.43 
  DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE 
                         4.08                          2.35 
[1] "0.0 - 30.7 (4.1)" "0.1 - 7.4 (2.3)" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 18(7Q36.2) MUTATED"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 18(7Q36.2) MUTATED"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 18(7Q36.2) MUTATED"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 18(7Q36.2) MUTATED"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 18(7Q36.2) WILD-TYPE"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 18(7Q36.2) MUTATED"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
  "DEL PEAK 18(7Q36.2) MUTATED"   "DEL PEAK 18(7Q36.2) MUTATED" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
  "DEL PEAK 18(7Q36.2) MUTATED" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 18(7Q36.2) WILD-TYPE" "DEL PEAK 18(7Q36.2) WILD-TYPE" 
                   TCGA-LN-A4A9 
"DEL PEAK 18(7Q36.2) WILD-TYPE" 
[1] "hr=" "5.2"
D41V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 18(7Q36.2) MUTATED          2         1         5          1
  DEL PEAK 18(7Q36.2) WILD-TYPE        0         2         2          3
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 18(7Q36.2) MUTATED            0          0
  DEL PEAK 18(7Q36.2) WILD-TYPE          2          1
D41V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 18(7Q36.2) MUTATED    4  3     2
  DEL PEAK 18(7Q36.2) WILD-TYPE  0  4     6
D41V4, multiclass
       clus
vv      DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE
  T1                              4                             0
  T2                              3                             4
  T3+T4                           2                             6
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 18(7Q36.2) MUTATED    4        5
  DEL PEAK 18(7Q36.2) WILD-TYPE  3        7
D41V5, multiclass
          clus
vv         DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE
  N0                                 4                             3
  N1+N2+N3                           5                             7
D41V6, binary
                               cls
clus                            0 1
  DEL PEAK 18(7Q36.2) MUTATED   2 7
  DEL PEAK 18(7Q36.2) WILD-TYPE 1 9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q36.2) MUTATED      2    7
  DEL PEAK 18(7Q36.2) WILD-TYPE    1    9
        clus
vv       DEL PEAK 18(7Q36.2) MUTATED DEL PEAK 18(7Q36.2) WILD-TYPE
  FEMALE                           2                             1
  MALE                             7                             9
D41V7, continuous

Clustering(42) Variable = DEL PEAK 19(8P23.2) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 19(8P23.2) MUTATED   6 1
  DEL PEAK 19(8P23.2) WILD-TYPE 4 4
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                            7                             8 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                            1                             4 
$`DEL PEAK 19(8P23.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OX 
        0.03         0.26         3.48         3.68         3.32         7.43 
TCGA-LN-A4A2 
        0.13 

$`DEL PEAK 19(8P23.2) WILD-TYPE`
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        4.08        18.35         1.38         3.16        30.71        29.00 
TCGA-L5-A4OW TCGA-LN-A4A9 
        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 
                         3.32                          5.59 
[1] "0.0 - 7.4 (3.3)"  "0.1 - 30.7 (5.6)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 19(8P23.2) MUTATED" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 19(8P23.2) MUTATED" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-LN-A4A9 
"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-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 19(8P23.2) MUTATED" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 19(8P23.2) WILD-TYPE" "DEL PEAK 19(8P23.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
  "DEL PEAK 19(8P23.2) MUTATED"   "DEL PEAK 19(8P23.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 19(8P23.2) WILD-TYPE" 
[1] "hr=" "1.3"
D42V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 19(8P23.2) MUTATED          0         1         4          2
  DEL PEAK 19(8P23.2) WILD-TYPE        2         2         3          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 19(8P23.2) MUTATED            2          1
  DEL PEAK 19(8P23.2) WILD-TYPE          0          0
D42V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 19(8P23.2) MUTATED    1  3     6
  DEL PEAK 19(8P23.2) WILD-TYPE  3  4     2
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                           6                             2
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 19(8P23.2) MUTATED    2        8
  DEL PEAK 19(8P23.2) WILD-TYPE  5        4
D42V5, multiclass
          clus
vv         DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  N0                                 2                             5
  N1+N2+N3                           8                             4
D42V6, binary
                               cls
clus                             0  1
  DEL PEAK 19(8P23.2) MUTATED    0 10
  DEL PEAK 19(8P23.2) WILD-TYPE  3  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.2) MUTATED      0   10
  DEL PEAK 19(8P23.2) WILD-TYPE    3    6
        clus
vv       DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  FEMALE                           0                             3
  MALE                            10                             6
D42V7, continuous

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

$`DEL PEAK 20(9P21.3) WILD-TYPE`
TCGA-L5-A4OE TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OX 
        3.48         1.38         3.16         7.43 

  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                          7.43 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                         3.68                          3.32 
[1] "0.0 - 30.7 (3.7)" "1.4 - 7.4 (3.3)" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 20(9P21.3) WILD-TYPE"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 20(9P21.3) WILD-TYPE"   "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-A4A2 
"DEL PEAK 20(9P21.3) WILD-TYPE"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 20(9P21.3) WILD-TYPE"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 20(9P21.3) WILD-TYPE"   "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-A4A2 
"DEL PEAK 20(9P21.3) WILD-TYPE"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-LN-A4A9 
  "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-L5-A4OE                    TCGA-L5-A4OF 
"DEL PEAK 20(9P21.3) WILD-TYPE"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 20(9P21.3) MUTATED"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
  "DEL PEAK 20(9P21.3) MUTATED" "DEL PEAK 20(9P21.3) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 20(9P21.3) WILD-TYPE"   "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-A4A2 
"DEL PEAK 20(9P21.3) WILD-TYPE"   "DEL PEAK 20(9P21.3) MUTATED" 
                   TCGA-LN-A4A9 
  "DEL PEAK 20(9P21.3) MUTATED" 
[1] "hr=" "8.1"
D43V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 20(9P21.3) MUTATED          1         3         6          3
  DEL PEAK 20(9P21.3) WILD-TYPE        1         0         1          1
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 20(9P21.3) MUTATED            1          1
  DEL PEAK 20(9P21.3) WILD-TYPE          1          0
D43V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 20(9P21.3) MUTATED    3  5     7
  DEL PEAK 20(9P21.3) WILD-TYPE  1  2     1
D43V4, multiclass
       clus
vv      DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  T1                              3                             1
  T2                              5                             2
  T3+T4                           7                             1
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 20(9P21.3) MUTATED    6        9
  DEL PEAK 20(9P21.3) WILD-TYPE  1        3
D43V5, multiclass
          clus
vv         DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  N0                                 6                             1
  N1+N2+N3                           9                             3
D43V6, binary
                               cls
clus                             0  1
  DEL PEAK 20(9P21.3) MUTATED    3 12
  DEL PEAK 20(9P21.3) WILD-TYPE  0  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9P21.3) MUTATED      3   12
  DEL PEAK 20(9P21.3) WILD-TYPE    0    4
        clus
vv       DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  FEMALE                           3                             0
  MALE                            12                             4
D43V7, continuous

Clustering(44) Variable = DEL PEAK 21(10P11.21) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 21(10P11.21) MUTATED   3 0
  DEL PEAK 21(10P11.21) WILD-TYPE 7 5
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                              3                              12 
  DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE 
                              0                               5 
$`DEL PEAK 21(10P11.21) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-LN-A4A9 
        0.03         3.48         0.07 

$`DEL PEAK 21(10P11.21) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.26         3.68         4.08        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 
        3.16        30.71        29.00         7.10         7.43         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 
                           0.07                            3.88 
[1] "0.0 - 3.5 (0.1)"  "0.1 - 30.7 (3.9)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 21(10P11.21) MUTATED" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
  "DEL PEAK 21(10P11.21) MUTATED" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-LN-A4A9 
  "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-L5-A4OE                      TCGA-L5-A4OF 
  "DEL PEAK 21(10P11.21) MUTATED" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-LN-A4A9 
  "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-L5-A4OE                      TCGA-L5-A4OF 
  "DEL PEAK 21(10P11.21) MUTATED" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 21(10P11.21) WILD-TYPE" "DEL PEAK 21(10P11.21) WILD-TYPE" 
                     TCGA-LN-A4A9 
  "DEL PEAK 21(10P11.21) MUTATED" 
[1] "hr="     "7.7e+07"
D44V2, continuous
                                 vv
clus                              STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 21(10P11.21) MUTATED          0         1         1          1
  DEL PEAK 21(10P11.21) WILD-TYPE        2         2         6          3
                                 vv
clus                              STAGE IIIB STAGE IIIC
  DEL PEAK 21(10P11.21) MUTATED            1          0
  DEL PEAK 21(10P11.21) WILD-TYPE          1          1
D44V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 21(10P11.21) MUTATED    0  2     2
  DEL PEAK 21(10P11.21) WILD-TYPE  4  5     6
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                             2                               6
                                 vv
clus                              N0 N1+N2+N3
  DEL PEAK 21(10P11.21) MUTATED    2        2
  DEL PEAK 21(10P11.21) WILD-TYPE  5       10
D44V5, multiclass
          clus
vv         DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE
  N0                                   2                               5
  N1+N2+N3                             2                              10
D44V6, binary
                                 cls
clus                               0  1
  DEL PEAK 21(10P11.21) MUTATED    0  4
  DEL PEAK 21(10P11.21) WILD-TYPE  3 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(10P11.21) MUTATED      0    4
  DEL PEAK 21(10P11.21) WILD-TYPE    3   12
        clus
vv       DEL PEAK 21(10P11.21) MUTATED DEL PEAK 21(10P11.21) WILD-TYPE
  FEMALE                             0                               3
  MALE                               4                              12
D44V7, continuous

Clustering(45) Variable = DEL PEAK 22(10Q23.31) MUTATION ANALYSIS
D45V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 22(10Q23.31) MUTATED   4 2
  DEL PEAK 22(10Q23.31) WILD-TYPE 6 3
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              6                               9 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              2                               3 
$`DEL PEAK 22(10Q23.31) MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-LN-A4A2 
        3.48         3.32         3.16        30.71         7.10         0.13 

$`DEL PEAK 22(10Q23.31) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.03         0.26         3.68         4.08        18.35         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A9 
       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 
                           3.40                            3.68 
[1] "0.1 - 30.7 (3.4)" "0.0 - 29.0 (3.7)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "DEL PEAK 22(10Q23.31) MUTATED"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-LN-A4A9 
"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-L5-A4OE                      TCGA-L5-A4OF 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "DEL PEAK 22(10Q23.31) MUTATED"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-LN-A4A9 
"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-L5-A4OE                      TCGA-L5-A4OF 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
"DEL PEAK 22(10Q23.31) WILD-TYPE" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
  "DEL PEAK 22(10Q23.31) MUTATED" "DEL PEAK 22(10Q23.31) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "DEL PEAK 22(10Q23.31) MUTATED"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 22(10Q23.31) WILD-TYPE"   "DEL PEAK 22(10Q23.31) MUTATED" 
                     TCGA-LN-A4A9 
"DEL PEAK 22(10Q23.31) WILD-TYPE" 
[1] "hr=" "1.1"
D45V2, continuous
                                 vv
clus                              STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 22(10Q23.31) MUTATED          1         1         2          2
  DEL PEAK 22(10Q23.31) WILD-TYPE        1         2         5          2
                                 vv
clus                              STAGE IIIB STAGE IIIC
  DEL PEAK 22(10Q23.31) MUTATED            1          1
  DEL PEAK 22(10Q23.31) WILD-TYPE          1          0
D45V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 22(10Q23.31) MUTATED    1  2     5
  DEL PEAK 22(10Q23.31) WILD-TYPE  3  5     3
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                             5                               3
                                 vv
clus                              N0 N1+N2+N3
  DEL PEAK 22(10Q23.31) MUTATED    3        5
  DEL PEAK 22(10Q23.31) WILD-TYPE  4        7
D45V5, multiclass
          clus
vv         DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  N0                                   3                               4
  N1+N2+N3                             5                               7
D45V6, binary
                                 cls
clus                               0  1
  DEL PEAK 22(10Q23.31) MUTATED    2  6
  DEL PEAK 22(10Q23.31) WILD-TYPE  1 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      2    6
  DEL PEAK 22(10Q23.31) WILD-TYPE    1   10
        clus
vv       DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  FEMALE                             2                               1
  MALE                               6                              10
D45V7, continuous

Clustering(46) Variable = DEL PEAK 23(11P15.4) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 23(11P15.4) MUTATED   2 1
  DEL PEAK 23(11P15.4) WILD-TYPE 8 4
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                             3                             12 
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                             1                              4 
$`DEL PEAK 23(11P15.4) MUTATED`
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-LN-A4A2 
        3.32         3.16         0.13 

$`DEL PEAK 23(11P15.4) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        0.03         0.26         3.48         3.68         4.08        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        1.38        30.71        29.00         7.10         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 
                          3.16                           3.88 
[1] "0.1 - 3.3 (3.2)"  "0.0 - 30.7 (3.9)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 23(11P15.4) WILD-TYPE"   "DEL PEAK 23(11P15.4) MUTATED" 
                    TCGA-LN-A4A9 
"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-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 23(11P15.4) WILD-TYPE"   "DEL PEAK 23(11P15.4) MUTATED" 
                    TCGA-LN-A4A9 
"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-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 23(11P15.4) MUTATED" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 23(11P15.4) WILD-TYPE"   "DEL PEAK 23(11P15.4) MUTATED" 
                    TCGA-LN-A4A9 
"DEL PEAK 23(11P15.4) WILD-TYPE" 
[1] "hr=" "4.2"
D46V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 23(11P15.4) MUTATED          1         1         0          2
  DEL PEAK 23(11P15.4) WILD-TYPE        1         2         7          2
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 23(11P15.4) MUTATED            0          1
  DEL PEAK 23(11P15.4) WILD-TYPE          2          0
D46V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 23(11P15.4) MUTATED    1  0     4
  DEL PEAK 23(11P15.4) WILD-TYPE  3  7     4
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                            4                              4
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 23(11P15.4) MUTATED    3        2
  DEL PEAK 23(11P15.4) WILD-TYPE  4       10
D46V5, multiclass
          clus
vv         DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE
  N0                                  3                              4
  N1+N2+N3                            2                             10
D46V6, binary
                                cls
clus                              0  1
  DEL PEAK 23(11P15.4) MUTATED    0  5
  DEL PEAK 23(11P15.4) WILD-TYPE  3 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.4) MUTATED      0    5
  DEL PEAK 23(11P15.4) WILD-TYPE    3   11
        clus
vv       DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE
  FEMALE                            0                              3
  MALE                              5                             11
D46V7, continuous
[1] "Remove cluster labels:"       "DEL PEAK 23(11P15.4) MUTATED"
clus
  DEL PEAK 23(11P15.4) MUTATED DEL PEAK 23(11P15.4) WILD-TYPE 
                             2                             10 
                    TCGA-IG-A3YA                     TCGA-IG-A4P3 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OM 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OQ 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A9 
"DEL PEAK 23(11P15.4) WILD-TYPE" "DEL PEAK 23(11P15.4) WILD-TYPE" 

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 3 4
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                             8                              7 
  DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE 
                             1                              4 
$`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-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        3.48        18.35         1.38        30.71         7.10         7.43 
TCGA-LN-A4A9 
        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                           7.10 
[1] "0.0 - 29.0 (3.2)" "0.1 - 30.7 (7.1)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 24(11Q24.3) MUTATED"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-LN-A4A9 
"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-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-LN-A4A9 
"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-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 24(11Q24.3) MUTATED" "DEL PEAK 24(11Q24.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 24(11Q24.3) WILD-TYPE"   "DEL PEAK 24(11Q24.3) MUTATED" 
                    TCGA-LN-A4A9 
"DEL PEAK 24(11Q24.3) WILD-TYPE" 
[1] "hr=" "2.2"
D47V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 24(11Q24.3) MUTATED          2         2         3          0
  DEL PEAK 24(11Q24.3) WILD-TYPE        0         1         4          4
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 24(11Q24.3) MUTATED            1          1
  DEL PEAK 24(11Q24.3) WILD-TYPE          1          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     4
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                              4
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 24(11Q24.3) MUTATED    4        5
  DEL PEAK 24(11Q24.3) WILD-TYPE  3        7
D47V5, multiclass
          clus
vv         DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE
  N0                                  4                              3
  N1+N2+N3                            5                              7
D47V6, binary
                                cls
clus                             0 1
  DEL PEAK 24(11Q24.3) MUTATED   1 8
  DEL PEAK 24(11Q24.3) WILD-TYPE 2 8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11Q24.3) MUTATED      1    8
  DEL PEAK 24(11Q24.3) WILD-TYPE    2    8
        clus
vv       DEL PEAK 24(11Q24.3) MUTATED DEL PEAK 24(11Q24.3) WILD-TYPE
  FEMALE                            1                              2
  MALE                              8                              8
D47V7, continuous

Clustering(48) Variable = DEL PEAK 25(12Q12) MUTATION ANALYSIS
D48V1, survival
                              sevent
clus2                          0 1
  DEL PEAK 25(12Q12) MUTATED   3 1
  DEL PEAK 25(12Q12) WILD-TYPE 7 4
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                           4                           11 
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                           1                            4 
$`DEL PEAK 25(12Q12) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OO TCGA-L5-A4OS TCGA-L5-A4OW 
        0.26         3.32        30.71         7.10 

$`DEL PEAK 25(12Q12) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.03         3.48         3.68         4.08        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.16        29.00         7.43         0.13         0.07 

  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                        0.26                         0.03 
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                       30.71                        29.00 
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                        5.21                         3.48 
[1] "0.3 - 30.7 (5.2)" "0.0 - 29.0 (3.5)"
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"DEL PEAK 25(12Q12) WILD-TYPE"   "DEL PEAK 25(12Q12) MUTATED" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
  "DEL PEAK 25(12Q12) MUTATED" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
"DEL PEAK 25(12Q12) WILD-TYPE"   "DEL PEAK 25(12Q12) MUTATED" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
"DEL PEAK 25(12Q12) WILD-TYPE"   "DEL PEAK 25(12Q12) MUTATED" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-LN-A4A9 
"DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"DEL PEAK 25(12Q12) WILD-TYPE"   "DEL PEAK 25(12Q12) MUTATED" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
  "DEL PEAK 25(12Q12) MUTATED" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
"DEL PEAK 25(12Q12) WILD-TYPE"   "DEL PEAK 25(12Q12) MUTATED" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
"DEL PEAK 25(12Q12) WILD-TYPE"   "DEL PEAK 25(12Q12) MUTATED" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-LN-A4A9 
"DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-IG-A4QS 
"DEL PEAK 25(12Q12) WILD-TYPE"   "DEL PEAK 25(12Q12) MUTATED" 
                  TCGA-L5-A4OE                   TCGA-L5-A4OF 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OO                   TCGA-L5-A4OQ 
  "DEL PEAK 25(12Q12) MUTATED" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OR                   TCGA-L5-A4OS 
"DEL PEAK 25(12Q12) WILD-TYPE"   "DEL PEAK 25(12Q12) MUTATED" 
                  TCGA-L5-A4OU                   TCGA-L5-A4OW 
"DEL PEAK 25(12Q12) WILD-TYPE"   "DEL PEAK 25(12Q12) MUTATED" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A2 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-LN-A4A9 
"DEL PEAK 25(12Q12) WILD-TYPE" 
[1] "hr=" "1.8"
D48V2, continuous
                              vv
clus                           STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 25(12Q12) MUTATED          0         0         2          1
  DEL PEAK 25(12Q12) WILD-TYPE        2         3         5          3
                              vv
clus                           STAGE IIIB STAGE IIIC
  DEL PEAK 25(12Q12) MUTATED            1          1
  DEL PEAK 25(12Q12) WILD-TYPE          1          0
D48V3, multiclass
                              vv
clus                           T1 T2 T3+T4
  DEL PEAK 25(12Q12) MUTATED    0  2     3
  DEL PEAK 25(12Q12) WILD-TYPE  4  5     5
D48V4, multiclass
       clus
vv      DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE
  T1                             0                            4
  T2                             2                            5
  T3+T4                          3                            5
                              vv
clus                           N0 N1+N2+N3
  DEL PEAK 25(12Q12) MUTATED    0        5
  DEL PEAK 25(12Q12) WILD-TYPE  7        7
D48V5, multiclass
          clus
vv         DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE
  N0                                0                            7
  N1+N2+N3                          5                            7
D48V6, binary
                              cls
clus                            0  1
  DEL PEAK 25(12Q12) MUTATED    2  3
  DEL PEAK 25(12Q12) WILD-TYPE  1 13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 25(12Q12) MUTATED      2    3
  DEL PEAK 25(12Q12) WILD-TYPE    1   13
        clus
vv       DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE
  FEMALE                          2                            1
  MALE                            3                           13
D48V7, continuous
[1] "Remove cluster labels:"     "DEL PEAK 25(12Q12) MUTATED"
clus
  DEL PEAK 25(12Q12) MUTATED DEL PEAK 25(12Q12) WILD-TYPE 
                           2                           10 
                  TCGA-IG-A3Y9                   TCGA-IG-A3YA 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-IG-A4P3                   TCGA-L5-A4OE 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OM                   TCGA-L5-A4ON 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OQ                   TCGA-L5-A4OU 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 
                  TCGA-L5-A4OX                   TCGA-LN-A4A9 
"DEL PEAK 25(12Q12) WILD-TYPE" "DEL PEAK 25(12Q12) WILD-TYPE" 

Clustering(49) Variable = DEL PEAK 26(13Q12.11) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 26(13Q12.11) MUTATED   6 1
  DEL PEAK 26(13Q12.11) WILD-TYPE 4 4
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                              7                               8 
  DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE 
                              1                               4 
$`DEL PEAK 26(13Q12.11) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-LN-A4A2 
        0.26         3.68         4.08         3.16        29.00         0.13 
TCGA-LN-A4A9 
        0.07 

$`DEL PEAK 26(13Q12.11) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.03         3.48        18.35         3.32         1.38        30.71 
TCGA-L5-A4OW TCGA-L5-A4OX 
        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 
                           3.16                            5.29 
[1] "0.1 - 29.0 (3.2)" "0.0 - 30.7 (5.3)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "DEL PEAK 26(13Q12.11) MUTATED" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "DEL PEAK 26(13Q12.11) MUTATED" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
  "DEL PEAK 26(13Q12.11) MUTATED" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-LN-A4A9 
  "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-L5-A4OE                      TCGA-L5-A4OF 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "DEL PEAK 26(13Q12.11) MUTATED" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "DEL PEAK 26(13Q12.11) MUTATED" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
  "DEL PEAK 26(13Q12.11) MUTATED" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-LN-A4A9 
  "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-L5-A4OE                      TCGA-L5-A4OF 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "DEL PEAK 26(13Q12.11) MUTATED" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 26(13Q12.11) WILD-TYPE" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "DEL PEAK 26(13Q12.11) MUTATED" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
  "DEL PEAK 26(13Q12.11) MUTATED" "DEL PEAK 26(13Q12.11) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 26(13Q12.11) WILD-TYPE"   "DEL PEAK 26(13Q12.11) MUTATED" 
                     TCGA-LN-A4A9 
  "DEL PEAK 26(13Q12.11) MUTATED" 
[1] "hr=" "1.8"
D49V2, continuous
                                 vv
clus                              STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 26(13Q12.11) MUTATED          2         3         2          3
  DEL PEAK 26(13Q12.11) WILD-TYPE        0         0         5          1
                                 vv
clus                              STAGE IIIB STAGE IIIC
  DEL PEAK 26(13Q12.11) MUTATED            1          0
  DEL PEAK 26(13Q12.11) WILD-TYPE          1          1
D49V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 26(13Q12.11) MUTATED    3  2     6
  DEL PEAK 26(13Q12.11) WILD-TYPE  1  5     2
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                             6                               2
                                 vv
clus                              N0 N1+N2+N3
  DEL PEAK 26(13Q12.11) MUTATED    7        4
  DEL PEAK 26(13Q12.11) WILD-TYPE  0        8
D49V5, multiclass
          clus
vv         DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE
  N0                                   7                               0
  N1+N2+N3                             4                               8
D49V6, binary
                                 cls
clus                               0  1
  DEL PEAK 26(13Q12.11) MUTATED    1 10
  DEL PEAK 26(13Q12.11) WILD-TYPE  2  6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(13Q12.11) MUTATED      1   10
  DEL PEAK 26(13Q12.11) WILD-TYPE    2    6
        clus
vv       DEL PEAK 26(13Q12.11) MUTATED DEL PEAK 26(13Q12.11) WILD-TYPE
  FEMALE                             1                               2
  MALE                              10                               6
D49V7, continuous

Clustering(50) Variable = DEL PEAK 27(15Q13.1) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 27(15Q13.1) MUTATED   4 0
  DEL PEAK 27(15Q13.1) WILD-TYPE 6 5
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                             4                             11 
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                             0                              5 
$`DEL PEAK 27(15Q13.1) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OU 
        0.26         3.48         4.08        29.00 

$`DEL PEAK 27(15Q13.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.03         3.68        18.35         3.32         1.38         3.16 
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 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                          3.78                           3.32 
[1] "0.3 - 29.0 (3.8)" "0.0 - 30.7 (3.3)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 27(15Q13.1) WILD-TYPE"   "DEL PEAK 27(15Q13.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 27(15Q13.1) MUTATED" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 27(15Q13.1) MUTATED" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 27(15Q13.1) WILD-TYPE" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 27(15Q13.1) WILD-TYPE" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 27(15Q13.1) MUTATED" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 27(15Q13.1) WILD-TYPE" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 27(15Q13.1) WILD-TYPE"   "DEL PEAK 27(15Q13.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 27(15Q13.1) MUTATED" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 27(15Q13.1) MUTATED" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 27(15Q13.1) WILD-TYPE" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 27(15Q13.1) WILD-TYPE" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 27(15Q13.1) MUTATED" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 27(15Q13.1) WILD-TYPE" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 27(15Q13.1) WILD-TYPE"   "DEL PEAK 27(15Q13.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 27(15Q13.1) MUTATED" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 27(15Q13.1) MUTATED" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 27(15Q13.1) WILD-TYPE" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 27(15Q13.1) WILD-TYPE" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 27(15Q13.1) MUTATED" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 27(15Q13.1) WILD-TYPE" "DEL PEAK 27(15Q13.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 27(15Q13.1) WILD-TYPE" 
[1] "hr="     "8.3e+08"
D50V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 27(15Q13.1) MUTATED          1         1         0          0
  DEL PEAK 27(15Q13.1) WILD-TYPE        1         2         7          4
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 27(15Q13.1) MUTATED            2          0
  DEL PEAK 27(15Q13.1) WILD-TYPE          0          1
D50V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 27(15Q13.1) MUTATED    1  0     3
  DEL PEAK 27(15Q13.1) WILD-TYPE  3  7     5
D50V4, multiclass
       clus
vv      DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE
  T1                               1                              3
  T2                               0                              7
  T3+T4                            3                              5
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 27(15Q13.1) MUTATED    2        2
  DEL PEAK 27(15Q13.1) WILD-TYPE  5       10
D50V5, multiclass
          clus
vv         DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE
  N0                                  2                              5
  N1+N2+N3                            2                             10
D50V6, binary
                                cls
clus                              0  1
  DEL PEAK 27(15Q13.1) MUTATED    1  3
  DEL PEAK 27(15Q13.1) WILD-TYPE  2 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q13.1) MUTATED      1    3
  DEL PEAK 27(15Q13.1) WILD-TYPE    2   13
        clus
vv       DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE
  FEMALE                            1                              2
  MALE                              3                             13
D50V7, continuous

Clustering(51) Variable = DEL PEAK 28(16Q23.1) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 28(16Q23.1) MUTATED   5 4
  DEL PEAK 28(16Q23.1) WILD-TYPE 5 1
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                             9                              6 
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                             4                              1 
$`DEL PEAK 28(16Q23.1) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS 
        0.26         3.48         3.68        18.35         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       29.00         7.10         7.43 

$`DEL PEAK 28(16Q23.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.03         4.08         3.32         1.38         0.13         0.07 

  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                         30.71                           4.08 
  DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE 
                         7.100                          0.755 
[1] "0.3 - 30.7 (7.1)" "0.0 - 4.1 (0.8)" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 28(16Q23.1) WILD-TYPE"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 28(16Q23.1) MUTATED"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 28(16Q23.1) WILD-TYPE"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 28(16Q23.1) WILD-TYPE" "DEL PEAK 28(16Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 28(16Q23.1) MUTATED"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 28(16Q23.1) MUTATED"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 28(16Q23.1) MUTATED" "DEL PEAK 28(16Q23.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 28(16Q23.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 28(16Q23.1) WILD-TYPE"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 28(16Q23.1) MUTATED"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 28(16Q23.1) WILD-TYPE"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 28(16Q23.1) WILD-TYPE" "DEL PEAK 28(16Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 28(16Q23.1) MUTATED"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 28(16Q23.1) MUTATED"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 28(16Q23.1) MUTATED" "DEL PEAK 28(16Q23.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 28(16Q23.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 28(16Q23.1) WILD-TYPE"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 28(16Q23.1) MUTATED"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 28(16Q23.1) WILD-TYPE"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 28(16Q23.1) WILD-TYPE" "DEL PEAK 28(16Q23.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 28(16Q23.1) MUTATED"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 28(16Q23.1) MUTATED"   "DEL PEAK 28(16Q23.1) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 28(16Q23.1) MUTATED" "DEL PEAK 28(16Q23.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 28(16Q23.1) WILD-TYPE" 
[1] "hr=" "3.3"
D51V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 28(16Q23.1) MUTATED          1         1         5          0
  DEL PEAK 28(16Q23.1) WILD-TYPE        1         2         2          4
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 28(16Q23.1) MUTATED            2          0
  DEL PEAK 28(16Q23.1) WILD-TYPE          0          1
D51V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 28(16Q23.1) MUTATED    3  3     3
  DEL PEAK 28(16Q23.1) WILD-TYPE  1  4     5
D51V4, multiclass
       clus
vv      DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE
  T1                               3                              1
  T2                               3                              4
  T3+T4                            3                              5
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 28(16Q23.1) MUTATED    2        7
  DEL PEAK 28(16Q23.1) WILD-TYPE  5        5
D51V5, multiclass
          clus
vv         DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE
  N0                                  2                              5
  N1+N2+N3                            7                              5
D51V6, binary
                                cls
clus                             0 1
  DEL PEAK 28(16Q23.1) MUTATED   2 7
  DEL PEAK 28(16Q23.1) WILD-TYPE 1 9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16Q23.1) MUTATED      2    7
  DEL PEAK 28(16Q23.1) WILD-TYPE    1    9
        clus
vv       DEL PEAK 28(16Q23.1) MUTATED DEL PEAK 28(16Q23.1) WILD-TYPE
  FEMALE                            2                              1
  MALE                              7                              9
D51V7, continuous

Clustering(52) Variable = DEL PEAK 29(17Q25.3) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 29(17Q25.3) MUTATED   2 1
  DEL PEAK 29(17Q25.3) WILD-TYPE 8 4
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                             3                             12 
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                             1                              4 
$`DEL PEAK 29(17Q25.3) MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OR TCGA-L5-A4OU 
        0.03         3.16        29.00 

$`DEL PEAK 29(17Q25.3) WILD-TYPE`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.48         3.68         4.08        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 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                          3.16                           3.58 
[1] "0.0 - 29.0 (3.2)" "0.1 - 30.7 (3.6)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 29(17Q25.3) MUTATED" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 29(17Q25.3) MUTATED" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 29(17Q25.3) MUTATED" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 29(17Q25.3) MUTATED" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 29(17Q25.3) MUTATED" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 29(17Q25.3) MUTATED" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 29(17Q25.3) MUTATED" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 29(17Q25.3) MUTATED" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 29(17Q25.3) MUTATED" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 29(17Q25.3) WILD-TYPE" 
[1] "hr=" "1.2"
D52V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 29(17Q25.3) MUTATED          1         1         1          0
  DEL PEAK 29(17Q25.3) WILD-TYPE        1         2         6          4
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 29(17Q25.3) MUTATED            0          0
  DEL PEAK 29(17Q25.3) WILD-TYPE          2          1
D52V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 29(17Q25.3) MUTATED    1  1     1
  DEL PEAK 29(17Q25.3) WILD-TYPE  3  6     7
D52V4, multiclass
       clus
vv      DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  T1                               1                              3
  T2                               1                              6
  T3+T4                            1                              7
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 29(17Q25.3) MUTATED    2        1
  DEL PEAK 29(17Q25.3) WILD-TYPE  5       11
D52V5, multiclass
          clus
vv         DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  N0                                  2                              5
  N1+N2+N3                            1                             11
D52V6, binary
                                cls
clus                              0  1
  DEL PEAK 29(17Q25.3) MUTATED    0  3
  DEL PEAK 29(17Q25.3) WILD-TYPE  3 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(17Q25.3) MUTATED      0    3
  DEL PEAK 29(17Q25.3) WILD-TYPE    3   13
        clus
vv       DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  FEMALE                            0                              3
  MALE                              3                             13
D52V7, continuous
[1] "Remove cluster labels:"       "DEL PEAK 29(17Q25.3) MUTATED"
clus
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                             2                             10 
                    TCGA-IG-A3Y9                     TCGA-IG-A3YA 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OM 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OW 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A9 
"DEL PEAK 29(17Q25.3) WILD-TYPE" "DEL PEAK 29(17Q25.3) WILD-TYPE" 

Clustering(53) Variable = DEL PEAK 30(18Q12.2) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 30(18Q12.2) MUTATED   5 2
  DEL PEAK 30(18Q12.2) WILD-TYPE 5 3
  DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE 
                             7                              8 
  DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE 
                             2                              3 
$`DEL PEAK 30(18Q12.2) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OU 
        0.26         3.48         3.68         3.32         3.16        29.00 
TCGA-L5-A4OX 
        7.43 

$`DEL PEAK 30(18Q12.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
        0.03         4.08        18.35         1.38        30.71         7.10 
TCGA-LN-A4A2 TCGA-LN-A4A9 
        0.13         0.07 

  DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE 
                          3.48                           2.73 
[1] "0.3 - 29.0 (3.5)" "0.0 - 30.7 (2.7)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 30(18Q12.2) WILD-TYPE"   "DEL PEAK 30(18Q12.2) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 30(18Q12.2) MUTATED"   "DEL PEAK 30(18Q12.2) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 30(18Q12.2) WILD-TYPE" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 30(18Q12.2) WILD-TYPE"   "DEL PEAK 30(18Q12.2) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 30(18Q12.2) MUTATED"   "DEL PEAK 30(18Q12.2) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 30(18Q12.2) WILD-TYPE" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 30(18Q12.2) WILD-TYPE"   "DEL PEAK 30(18Q12.2) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 30(18Q12.2) MUTATED"   "DEL PEAK 30(18Q12.2) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 30(18Q12.2) WILD-TYPE" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 30(18Q12.2) MUTATED" "DEL PEAK 30(18Q12.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 30(18Q12.2) WILD-TYPE" 
[1] "hr=" "1.4"
D53V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 30(18Q12.2) MUTATED          1         1         2          2
  DEL PEAK 30(18Q12.2) WILD-TYPE        1         2         5          2
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 30(18Q12.2) MUTATED            2          1
  DEL PEAK 30(18Q12.2) WILD-TYPE          0          0
D53V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 30(18Q12.2) MUTATED    2  1     6
  DEL PEAK 30(18Q12.2) WILD-TYPE  2  6     2
D53V4, multiclass
       clus
vv      DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE
  T1                               2                              2
  T2                               1                              6
  T3+T4                            6                              2
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 30(18Q12.2) MUTATED    3        6
  DEL PEAK 30(18Q12.2) WILD-TYPE  4        6
D53V5, multiclass
          clus
vv         DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE
  N0                                  3                              4
  N1+N2+N3                            6                              6
D53V6, binary
                                cls
clus                             0 1
  DEL PEAK 30(18Q12.2) MUTATED   0 9
  DEL PEAK 30(18Q12.2) WILD-TYPE 3 7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q12.2) MUTATED      0    9
  DEL PEAK 30(18Q12.2) WILD-TYPE    3    7
        clus
vv       DEL PEAK 30(18Q12.2) MUTATED DEL PEAK 30(18Q12.2) WILD-TYPE
  FEMALE                            0                              3
  MALE                              9                              7
D53V7, continuous

Clustering(54) Variable = DEL PEAK 31(18Q21.2) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 31(18Q21.2) MUTATED   6 2
  DEL PEAK 31(18Q21.2) WILD-TYPE 4 3
  DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE 
                             8                              7 
  DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE 
                             2                              3 
$`DEL PEAK 31(18Q21.2) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OR 
        0.03         0.26         3.48         3.68         3.32         3.16 
TCGA-L5-A4OU TCGA-L5-A4OX 
       29.00         7.43 

$`DEL PEAK 31(18Q21.2) WILD-TYPE`
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-LN-A4A2 
        4.08        18.35         1.38        30.71         7.10         0.13 
TCGA-LN-A4A9 
        0.07 

  DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE 
                         29.00                          30.71 
  DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE 
                          3.40                           4.08 
[1] "0.0 - 29.0 (3.4)" "0.1 - 30.7 (4.1)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 31(18Q21.2) MUTATED"   "DEL PEAK 31(18Q21.2) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 31(18Q21.2) MUTATED"   "DEL PEAK 31(18Q21.2) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 31(18Q21.2) WILD-TYPE" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 31(18Q21.2) MUTATED"   "DEL PEAK 31(18Q21.2) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 31(18Q21.2) MUTATED"   "DEL PEAK 31(18Q21.2) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 31(18Q21.2) WILD-TYPE" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 31(18Q21.2) MUTATED"   "DEL PEAK 31(18Q21.2) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 31(18Q21.2) MUTATED"   "DEL PEAK 31(18Q21.2) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 31(18Q21.2) WILD-TYPE" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 31(18Q21.2) MUTATED" "DEL PEAK 31(18Q21.2) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 31(18Q21.2) WILD-TYPE" 
[1] "hr=" "1.4"
D54V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 31(18Q21.2) MUTATED          1         1         3          2
  DEL PEAK 31(18Q21.2) WILD-TYPE        1         2         4          2
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 31(18Q21.2) MUTATED            2          1
  DEL PEAK 31(18Q21.2) WILD-TYPE          0          0
D54V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 31(18Q21.2) MUTATED    2  2     6
  DEL PEAK 31(18Q21.2) WILD-TYPE  2  5     2
D54V4, multiclass
       clus
vv      DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE
  T1                               2                              2
  T2                               2                              5
  T3+T4                            6                              2
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 31(18Q21.2) MUTATED    3        7
  DEL PEAK 31(18Q21.2) WILD-TYPE  4        5
D54V5, multiclass
          clus
vv         DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE
  N0                                  3                              4
  N1+N2+N3                            7                              5
D54V6, binary
                                cls
clus                              0  1
  DEL PEAK 31(18Q21.2) MUTATED    0 10
  DEL PEAK 31(18Q21.2) WILD-TYPE  3  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q21.2) MUTATED      0   10
  DEL PEAK 31(18Q21.2) WILD-TYPE    3    6
        clus
vv       DEL PEAK 31(18Q21.2) MUTATED DEL PEAK 31(18Q21.2) WILD-TYPE
  FEMALE                            0                              3
  MALE                             10                              6
D54V7, continuous

Clustering(55) Variable = DEL PEAK 32(19P13.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 32(19P13.3) MUTATED   8 2
  DEL PEAK 32(19P13.3) WILD-TYPE 2 3
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            10                              5 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                             2                              3 
$`DEL PEAK 32(19P13.3) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO 
        0.03         0.26         3.48         3.68         4.08         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX TCGA-LN-A4A2 
        1.38        30.71         7.43         0.13 

$`DEL PEAK 32(19P13.3) WILD-TYPE`
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-LN-A4A9 
       18.35         3.16        29.00         7.10         0.07 

  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                         30.71                          29.00 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                           3.4                            7.1 
[1] "0.0 - 30.7 (3.4)" "0.1 - 29.0 (7.1)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 32(19P13.3) MUTATED" "DEL PEAK 32(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 32(19P13.3) WILD-TYPE"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 32(19P13.3) WILD-TYPE" "DEL PEAK 32(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-LN-A4A9 
"DEL PEAK 32(19P13.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 32(19P13.3) MUTATED" "DEL PEAK 32(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 32(19P13.3) WILD-TYPE"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 32(19P13.3) WILD-TYPE" "DEL PEAK 32(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-LN-A4A9 
"DEL PEAK 32(19P13.3) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 32(19P13.3) MUTATED" "DEL PEAK 32(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 32(19P13.3) WILD-TYPE"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 32(19P13.3) WILD-TYPE" "DEL PEAK 32(19P13.3) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
  "DEL PEAK 32(19P13.3) MUTATED"   "DEL PEAK 32(19P13.3) MUTATED" 
                    TCGA-LN-A4A9 
"DEL PEAK 32(19P13.3) WILD-TYPE" 
[1] "hr=" "1.5"
D55V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 32(19P13.3) MUTATED          1         1         5          2
  DEL PEAK 32(19P13.3) WILD-TYPE        1         2         2          2
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 32(19P13.3) MUTATED            2          1
  DEL PEAK 32(19P13.3) WILD-TYPE          0          0
D55V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 32(19P13.3) MUTATED    2  5     5
  DEL PEAK 32(19P13.3) WILD-TYPE  2  2     3
D55V4, multiclass
       clus
vv      DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  T1                               2                              2
  T2                               5                              2
  T3+T4                            5                              3
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 32(19P13.3) MUTATED    2       10
  DEL PEAK 32(19P13.3) WILD-TYPE  5        2
D55V5, multiclass
          clus
vv         DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  N0                                  2                              5
  N1+N2+N3                           10                              2
D55V6, binary
                                cls
clus                              0  1
  DEL PEAK 32(19P13.3) MUTATED    2 10
  DEL PEAK 32(19P13.3) WILD-TYPE  1  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED      2   10
  DEL PEAK 32(19P13.3) WILD-TYPE    1    6
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  FEMALE                            2                              1
  MALE                             10                              6
D55V7, continuous

Clustering(56) Variable = DEL PEAK 33(19Q13.31) MUTATION ANALYSIS
D56V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 33(19Q13.31) MUTATED   3 0
  DEL PEAK 33(19Q13.31) WILD-TYPE 7 5
  DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE 
                              3                              12 
  DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE 
                              0                               5 
$`DEL PEAK 33(19Q13.31) MUTATED`
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-LN-A4A2 
        4.08        30.71         0.13 

$`DEL PEAK 33(19Q13.31) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.48         3.68        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
        1.38         3.16        29.00         7.10         7.43         0.07 

  DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE 
                           0.13                            0.03 
  DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE 
                          30.71                           29.00 
  DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE 
                           4.08                            3.40 
[1] "0.1 - 30.7 (4.1)" "0.0 - 29.0 (3.4)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "DEL PEAK 33(19Q13.31) MUTATED" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
"DEL PEAK 33(19Q13.31) WILD-TYPE"   "DEL PEAK 33(19Q13.31) MUTATED" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 33(19Q13.31) WILD-TYPE"   "DEL PEAK 33(19Q13.31) MUTATED" 
                     TCGA-LN-A4A9 
"DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "DEL PEAK 33(19Q13.31) MUTATED" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
"DEL PEAK 33(19Q13.31) WILD-TYPE"   "DEL PEAK 33(19Q13.31) MUTATED" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 33(19Q13.31) WILD-TYPE"   "DEL PEAK 33(19Q13.31) MUTATED" 
                     TCGA-LN-A4A9 
"DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "DEL PEAK 33(19Q13.31) MUTATED" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
"DEL PEAK 33(19Q13.31) WILD-TYPE"   "DEL PEAK 33(19Q13.31) MUTATED" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
"DEL PEAK 33(19Q13.31) WILD-TYPE"   "DEL PEAK 33(19Q13.31) MUTATED" 
                     TCGA-LN-A4A9 
"DEL PEAK 33(19Q13.31) WILD-TYPE" 
[1] "hr="     "7.7e+08"
D56V2, continuous
                                 vv
clus                              STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 33(19Q13.31) MUTATED          1         1         1          1
  DEL PEAK 33(19Q13.31) WILD-TYPE        1         2         6          3
                                 vv
clus                              STAGE IIIB STAGE IIIC
  DEL PEAK 33(19Q13.31) MUTATED            0          0
  DEL PEAK 33(19Q13.31) WILD-TYPE          2          1
D56V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 33(19Q13.31) MUTATED    1  1     2
  DEL PEAK 33(19Q13.31) WILD-TYPE  3  6     6
D56V4, multiclass
       clus
vv      DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE
  T1                                1                               3
  T2                                1                               6
  T3+T4                             2                               6
                                 vv
clus                              N0 N1+N2+N3
  DEL PEAK 33(19Q13.31) MUTATED    2        2
  DEL PEAK 33(19Q13.31) WILD-TYPE  5       10
D56V5, multiclass
          clus
vv         DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE
  N0                                   2                               5
  N1+N2+N3                             2                              10
D56V6, binary
                                 cls
clus                               0  1
  DEL PEAK 33(19Q13.31) MUTATED    2  2
  DEL PEAK 33(19Q13.31) WILD-TYPE  1 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19Q13.31) MUTATED      2    2
  DEL PEAK 33(19Q13.31) WILD-TYPE    1   14
        clus
vv       DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE
  FEMALE                             2                               1
  MALE                               2                              14
D56V7, continuous
[1] "Remove cluster labels:"        "DEL PEAK 33(19Q13.31) MUTATED"
clus
  DEL PEAK 33(19Q13.31) MUTATED DEL PEAK 33(19Q13.31) WILD-TYPE 
                              1                              11 
                     TCGA-IG-A3Y9                      TCGA-IG-A3YA 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-L5-A4OE 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4ON                      TCGA-L5-A4OO 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OQ                      TCGA-L5-A4OU 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-L5-A4OW                      TCGA-L5-A4OX 
"DEL PEAK 33(19Q13.31) WILD-TYPE" "DEL PEAK 33(19Q13.31) WILD-TYPE" 
                     TCGA-LN-A4A9 
"DEL PEAK 33(19Q13.31) WILD-TYPE" 

Clustering(57) Variable = DEL PEAK 34(20P12.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 34(20P12.1) MUTATED   3 0
  DEL PEAK 34(20P12.1) WILD-TYPE 7 5
  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                             3                             12 
  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                             0                              5 
$`DEL PEAK 34(20P12.1) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OF TCGA-L5-A4OO 
        0.26         3.68         3.32 

$`DEL PEAK 34(20P12.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.03         3.48         4.08        18.35         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A2 TCGA-LN-A4A9 
       30.71        29.00         7.10         7.43         0.13         0.07 

  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                          0.26                           0.03 
  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                          3.68                          30.71 
  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                          3.32                           3.78 
[1] "0.3 - 3.7 (3.3)"  "0.0 - 30.7 (3.8)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 34(20P12.1) WILD-TYPE"   "DEL PEAK 34(20P12.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 34(20P12.1) WILD-TYPE"   "DEL PEAK 34(20P12.1) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 34(20P12.1) MUTATED" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 34(20P12.1) WILD-TYPE"   "DEL PEAK 34(20P12.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 34(20P12.1) WILD-TYPE"   "DEL PEAK 34(20P12.1) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 34(20P12.1) MUTATED" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 34(20P12.1) WILD-TYPE"   "DEL PEAK 34(20P12.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 34(20P12.1) WILD-TYPE"   "DEL PEAK 34(20P12.1) MUTATED" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
  "DEL PEAK 34(20P12.1) MUTATED" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 34(20P12.1) WILD-TYPE" 
[1] "hr="     "2.5e+08"
D57V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 34(20P12.1) MUTATED          0         0         1          0
  DEL PEAK 34(20P12.1) WILD-TYPE        2         3         6          4
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 34(20P12.1) MUTATED            1          1
  DEL PEAK 34(20P12.1) WILD-TYPE          1          0
D57V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 34(20P12.1) MUTATED    1  0     2
  DEL PEAK 34(20P12.1) WILD-TYPE  3  7     6
D57V4, multiclass
       clus
vv      DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE
  T1                               1                              3
  T2                               0                              7
  T3+T4                            2                              6
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 34(20P12.1) MUTATED    0        3
  DEL PEAK 34(20P12.1) WILD-TYPE  7        9
D57V5, multiclass
          clus
vv         DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE
  N0                                  0                              7
  N1+N2+N3                            3                              9
D57V6, binary
                                cls
clus                              0  1
  DEL PEAK 34(20P12.1) MUTATED    0  3
  DEL PEAK 34(20P12.1) WILD-TYPE  3 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(20P12.1) MUTATED      0    3
  DEL PEAK 34(20P12.1) WILD-TYPE    3   13
        clus
vv       DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE
  FEMALE                            0                              3
  MALE                              3                             13
D57V7, continuous
[1] "Remove cluster labels:"       "DEL PEAK 34(20P12.1) MUTATED"
clus
  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                             1                             11 
                    TCGA-IG-A3Y9                     TCGA-IG-A3YA 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-L5-A4OE 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OU 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 34(20P12.1) WILD-TYPE" "DEL PEAK 34(20P12.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 34(20P12.1) WILD-TYPE" 

Clustering(58) Variable = DEL PEAK 35(21Q22.12) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                             0 1
  DEL PEAK 35(21Q22.12) MUTATED   6 3
  DEL PEAK 35(21Q22.12) WILD-TYPE 4 2
  DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE 
                              9                               6 
  DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE 
                              3                               2 
$`DEL PEAK 35(21Q22.12) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OS 
        0.03         0.26         3.48         4.08         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       29.00         7.10         7.43 

$`DEL PEAK 35(21Q22.12) WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-LN-A4A2 TCGA-LN-A4A9 
        3.68        18.35         3.32         1.38         0.13         0.07 

  DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE 
                           0.03                            0.07 
  DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE 
                          30.71                           18.35 
  DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE 
                           4.08                            2.35 
[1] "0.0 - 30.7 (4.1)" "0.1 - 18.4 (2.3)"
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 35(21Q22.12) MUTATED"   "DEL PEAK 35(21Q22.12) MUTATED" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
  "DEL PEAK 35(21Q22.12) MUTATED" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "DEL PEAK 35(21Q22.12) MUTATED" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 35(21Q22.12) WILD-TYPE" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "DEL PEAK 35(21Q22.12) MUTATED"   "DEL PEAK 35(21Q22.12) MUTATED" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
  "DEL PEAK 35(21Q22.12) MUTATED"   "DEL PEAK 35(21Q22.12) MUTATED" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
  "DEL PEAK 35(21Q22.12) MUTATED" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-LN-A4A9 
"DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 35(21Q22.12) MUTATED"   "DEL PEAK 35(21Q22.12) MUTATED" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
  "DEL PEAK 35(21Q22.12) MUTATED" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "DEL PEAK 35(21Q22.12) MUTATED" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 35(21Q22.12) WILD-TYPE" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "DEL PEAK 35(21Q22.12) MUTATED"   "DEL PEAK 35(21Q22.12) MUTATED" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
  "DEL PEAK 35(21Q22.12) MUTATED"   "DEL PEAK 35(21Q22.12) MUTATED" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
  "DEL PEAK 35(21Q22.12) MUTATED" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-LN-A4A9 
"DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-IG-A4P3                      TCGA-IG-A4QS 
  "DEL PEAK 35(21Q22.12) MUTATED"   "DEL PEAK 35(21Q22.12) MUTATED" 
                     TCGA-L5-A4OE                      TCGA-L5-A4OF 
  "DEL PEAK 35(21Q22.12) MUTATED" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OM                      TCGA-L5-A4ON 
  "DEL PEAK 35(21Q22.12) MUTATED" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OO                      TCGA-L5-A4OQ 
"DEL PEAK 35(21Q22.12) WILD-TYPE" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-L5-A4OR                      TCGA-L5-A4OS 
  "DEL PEAK 35(21Q22.12) MUTATED"   "DEL PEAK 35(21Q22.12) MUTATED" 
                     TCGA-L5-A4OU                      TCGA-L5-A4OW 
  "DEL PEAK 35(21Q22.12) MUTATED"   "DEL PEAK 35(21Q22.12) MUTATED" 
                     TCGA-L5-A4OX                      TCGA-LN-A4A2 
  "DEL PEAK 35(21Q22.12) MUTATED" "DEL PEAK 35(21Q22.12) WILD-TYPE" 
                     TCGA-LN-A4A9 
"DEL PEAK 35(21Q22.12) WILD-TYPE" 
[1] "hr=" "1.7"
D58V2, continuous
                                 vv
clus                              STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 35(21Q22.12) MUTATED          2         1         4          2
  DEL PEAK 35(21Q22.12) WILD-TYPE        0         2         3          2
                                 vv
clus                              STAGE IIIB STAGE IIIC
  DEL PEAK 35(21Q22.12) MUTATED            2          0
  DEL PEAK 35(21Q22.12) WILD-TYPE          0          1
D58V3, multiclass
                                 vv
clus                              T1 T2 T3+T4
  DEL PEAK 35(21Q22.12) MUTATED    2  4     5
  DEL PEAK 35(21Q22.12) WILD-TYPE  2  3     3
D58V4, multiclass
       clus
vv      DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE
  T1                                2                               2
  T2                                4                               3
  T3+T4                             5                               3
                                 vv
clus                              N0 N1+N2+N3
  DEL PEAK 35(21Q22.12) MUTATED    5        6
  DEL PEAK 35(21Q22.12) WILD-TYPE  2        6
D58V5, multiclass
          clus
vv         DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE
  N0                                   5                               2
  N1+N2+N3                             6                               6
D58V6, binary
                                 cls
clus                              0 1
  DEL PEAK 35(21Q22.12) MUTATED   3 8
  DEL PEAK 35(21Q22.12) WILD-TYPE 0 8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(21Q22.12) MUTATED      3    8
  DEL PEAK 35(21Q22.12) WILD-TYPE    0    8
        clus
vv       DEL PEAK 35(21Q22.12) MUTATED DEL PEAK 35(21Q22.12) WILD-TYPE
  FEMALE                             3                               0
  MALE                               8                               8
D58V7, continuous

Clustering(59) Variable = DEL PEAK 36(22Q11.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 36(22Q11.1) MUTATED   5 3
  DEL PEAK 36(22Q11.1) WILD-TYPE 5 2
  DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE 
                             8                              7 
  DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE 
                             3                              2 
$`DEL PEAK 36(22Q11.1) MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS 
        0.03         0.26         3.48        18.35         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW 
       29.00         7.10 

$`DEL PEAK 36(22Q11.1) WILD-TYPE`
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-LN-A4A2 
        3.68         4.08         3.32         1.38         7.43         0.13 
TCGA-LN-A4A9 
        0.07 

  DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE 
                         30.71                           7.43 
  DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE 
                          5.29                           3.32 
[1] "0.0 - 30.7 (5.3)" "0.1 - 7.4 (3.3)" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 36(22Q11.1) MUTATED"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 36(22Q11.1) MUTATED" "DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 36(22Q11.1) WILD-TYPE"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 36(22Q11.1) WILD-TYPE" "DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 36(22Q11.1) MUTATED"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 36(22Q11.1) MUTATED"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 36(22Q11.1) WILD-TYPE" "DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 36(22Q11.1) MUTATED"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 36(22Q11.1) MUTATED" "DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 36(22Q11.1) WILD-TYPE"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 36(22Q11.1) WILD-TYPE" "DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 36(22Q11.1) MUTATED"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 36(22Q11.1) MUTATED"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 36(22Q11.1) WILD-TYPE" "DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
  "DEL PEAK 36(22Q11.1) MUTATED"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
  "DEL PEAK 36(22Q11.1) MUTATED" "DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
"DEL PEAK 36(22Q11.1) WILD-TYPE"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 36(22Q11.1) WILD-TYPE" "DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 36(22Q11.1) MUTATED"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
  "DEL PEAK 36(22Q11.1) MUTATED"   "DEL PEAK 36(22Q11.1) MUTATED" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 36(22Q11.1) WILD-TYPE" "DEL PEAK 36(22Q11.1) WILD-TYPE" 
                    TCGA-LN-A4A9 
"DEL PEAK 36(22Q11.1) WILD-TYPE" 
[1] "hr=" "2.2"
D59V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 36(22Q11.1) MUTATED          1         1         4          1
  DEL PEAK 36(22Q11.1) WILD-TYPE        1         2         3          3
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 36(22Q11.1) MUTATED            2          0
  DEL PEAK 36(22Q11.1) WILD-TYPE          0          1
D59V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 36(22Q11.1) MUTATED    2  3     4
  DEL PEAK 36(22Q11.1) WILD-TYPE  2  4     4
D59V4, multiclass
       clus
vv      DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE
  T1                               2                              2
  T2                               3                              4
  T3+T4                            4                              4
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 36(22Q11.1) MUTATED    2        7
  DEL PEAK 36(22Q11.1) WILD-TYPE  5        5
D59V5, multiclass
          clus
vv         DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE
  N0                                  2                              5
  N1+N2+N3                            7                              5
D59V6, binary
                                cls
clus                             0 1
  DEL PEAK 36(22Q11.1) MUTATED   2 7
  DEL PEAK 36(22Q11.1) WILD-TYPE 1 9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(22Q11.1) MUTATED      2    7
  DEL PEAK 36(22Q11.1) WILD-TYPE    1    9
        clus
vv       DEL PEAK 36(22Q11.1) MUTATED DEL PEAK 36(22Q11.1) WILD-TYPE
  FEMALE                            2                              1
  MALE                              7                              9
D59V7, continuous

Clustering(60) Variable = DEL PEAK 37(XP22.2) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 37(XP22.2) MUTATED   4 1
  DEL PEAK 37(XP22.2) WILD-TYPE 6 4
  DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE 
                            5                            10 
  DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE 
                            1                             4 
$`DEL PEAK 37(XP22.2) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-LN-A4A2 
        0.26         3.48         3.68        18.35         0.13 

$`DEL PEAK 37(XP22.2) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        0.03         4.08         3.32         1.38         3.16        30.71 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-LN-A4A9 
       29.00         7.10         7.43         0.07 

  DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE 
                        18.35                         30.71 
  DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE 
                         3.48                          3.70 
[1] "0.1 - 18.4 (3.5)" "0.0 - 30.7 (3.7)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 37(XP22.2) WILD-TYPE"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 37(XP22.2) MUTATED"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 37(XP22.2) WILD-TYPE"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 37(XP22.2) WILD-TYPE" "DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 37(XP22.2) WILD-TYPE" "DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 37(XP22.2) WILD-TYPE" "DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 37(XP22.2) WILD-TYPE"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 37(XP22.2) WILD-TYPE"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 37(XP22.2) MUTATED"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 37(XP22.2) WILD-TYPE"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 37(XP22.2) WILD-TYPE" "DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 37(XP22.2) WILD-TYPE" "DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 37(XP22.2) WILD-TYPE" "DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 37(XP22.2) WILD-TYPE"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 37(XP22.2) WILD-TYPE"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 37(XP22.2) MUTATED"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
"DEL PEAK 37(XP22.2) WILD-TYPE"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 37(XP22.2) WILD-TYPE" "DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 37(XP22.2) WILD-TYPE" "DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 37(XP22.2) WILD-TYPE" "DEL PEAK 37(XP22.2) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 37(XP22.2) WILD-TYPE"   "DEL PEAK 37(XP22.2) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 37(XP22.2) WILD-TYPE" 
[1] "hr=" "1.5"
D60V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 37(XP22.2) MUTATED          0         1         3          1
  DEL PEAK 37(XP22.2) WILD-TYPE        2         2         4          3
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 37(XP22.2) MUTATED            2          0
  DEL PEAK 37(XP22.2) WILD-TYPE          0          1
D60V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 37(XP22.2) MUTATED    2  1     4
  DEL PEAK 37(XP22.2) WILD-TYPE  2  6     4
D60V4, multiclass
       clus
vv      DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE
  T1                              2                             2
  T2                              1                             6
  T3+T4                           4                             4
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 37(XP22.2) MUTATED    2        5
  DEL PEAK 37(XP22.2) WILD-TYPE  5        7
D60V5, multiclass
          clus
vv         DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE
  N0                                 2                             5
  N1+N2+N3                           5                             7
D60V6, binary
                               cls
clus                            0 1
  DEL PEAK 37(XP22.2) MUTATED   0 7
  DEL PEAK 37(XP22.2) WILD-TYPE 3 9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 37(XP22.2) MUTATED      0    7
  DEL PEAK 37(XP22.2) WILD-TYPE    3    9
        clus
vv       DEL PEAK 37(XP22.2) MUTATED DEL PEAK 37(XP22.2) WILD-TYPE
  FEMALE                           0                             3
  MALE                             7                             9
D60V7, continuous

Clustering(61) Variable = DEL PEAK 38(XP21.1) MUTATION ANALYSIS
D61V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 38(XP21.1) MUTATED   5 2
  DEL PEAK 38(XP21.1) WILD-TYPE 5 3
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                            7                             8 
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                            2                             3 
$`DEL PEAK 38(XP21.1) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.26         3.48         3.68         4.08        18.35         1.38 
TCGA-LN-A4A2 
        0.13 

$`DEL PEAK 38(XP21.1) WILD-TYPE`
TCGA-IG-A4P3 TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        0.03         3.32         3.16        30.71        29.00         7.10 
TCGA-L5-A4OX TCGA-LN-A4A9 
        7.43         0.07 

  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                        18.35                         30.71 
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                         3.48                          5.21 
[1] "0.1 - 18.4 (3.5)" "0.0 - 30.7 (5.2)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 38(XP21.1) WILD-TYPE"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 38(XP21.1) MUTATED"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 38(XP21.1) MUTATED"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 38(XP21.1) WILD-TYPE"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 38(XP21.1) WILD-TYPE" "DEL PEAK 38(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 38(XP21.1) WILD-TYPE" "DEL PEAK 38(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 38(XP21.1) WILD-TYPE"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 38(XP21.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 38(XP21.1) WILD-TYPE"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 38(XP21.1) MUTATED"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 38(XP21.1) MUTATED"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 38(XP21.1) WILD-TYPE"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 38(XP21.1) WILD-TYPE" "DEL PEAK 38(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 38(XP21.1) WILD-TYPE" "DEL PEAK 38(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 38(XP21.1) WILD-TYPE"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 38(XP21.1) WILD-TYPE" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 38(XP21.1) WILD-TYPE"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 38(XP21.1) MUTATED"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 38(XP21.1) MUTATED"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 38(XP21.1) WILD-TYPE"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 38(XP21.1) WILD-TYPE" "DEL PEAK 38(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 38(XP21.1) WILD-TYPE" "DEL PEAK 38(XP21.1) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 38(XP21.1) WILD-TYPE"   "DEL PEAK 38(XP21.1) MUTATED" 
                   TCGA-LN-A4A9 
"DEL PEAK 38(XP21.1) WILD-TYPE" 
[1] "hr=" "1.4"
D61V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 38(XP21.1) MUTATED          1         1         3          3
  DEL PEAK 38(XP21.1) WILD-TYPE        1         2         4          1
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 38(XP21.1) MUTATED            2          0
  DEL PEAK 38(XP21.1) WILD-TYPE          0          1
D61V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 38(XP21.1) MUTATED    3  2     5
  DEL PEAK 38(XP21.1) WILD-TYPE  1  5     3
D61V4, multiclass
       clus
vv      DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE
  T1                              3                             1
  T2                              2                             5
  T3+T4                           5                             3
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 38(XP21.1) MUTATED    4        6
  DEL PEAK 38(XP21.1) WILD-TYPE  3        6
D61V5, multiclass
          clus
vv         DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE
  N0                                 4                             3
  N1+N2+N3                           6                             6
D61V6, binary
                               cls
clus                            0 1
  DEL PEAK 38(XP21.1) MUTATED   1 9
  DEL PEAK 38(XP21.1) WILD-TYPE 2 7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 38(XP21.1) MUTATED      1    9
  DEL PEAK 38(XP21.1) WILD-TYPE    2    7
        clus
vv       DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE
  FEMALE                           1                             2
  MALE                             9                             7
D61V7, continuous

Clustering(62) Variable = DEL PEAK 39(XP11.3) MUTATION ANALYSIS
D62V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 39(XP11.3) MUTATED   6 1
  DEL PEAK 39(XP11.3) WILD-TYPE 4 4
  DEL PEAK 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE 
                            7                             8 
  DEL PEAK 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE 
                            1                             4 
$`DEL PEAK 39(XP11.3) MUTATED`
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-LN-A4A2 
        0.26         3.48         3.68         4.08        18.35         0.13 
TCGA-LN-A4A9 
        0.07 

$`DEL PEAK 39(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 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE 
                        18.35                         30.71 
  DEL PEAK 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE 
                         3.48                          5.21 
[1] "0.1 - 18.4 (3.5)" "0.0 - 30.7 (5.2)"
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 39(XP11.3) WILD-TYPE"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 39(XP11.3) MUTATED"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 39(XP11.3) MUTATED"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 39(XP11.3) WILD-TYPE" "DEL PEAK 39(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 39(XP11.3) WILD-TYPE" "DEL PEAK 39(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 39(XP11.3) WILD-TYPE" "DEL PEAK 39(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 39(XP11.3) WILD-TYPE"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-LN-A4A9 
  "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 39(XP11.3) WILD-TYPE"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 39(XP11.3) MUTATED"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 39(XP11.3) MUTATED"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 39(XP11.3) WILD-TYPE" "DEL PEAK 39(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 39(XP11.3) WILD-TYPE" "DEL PEAK 39(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 39(XP11.3) WILD-TYPE" "DEL PEAK 39(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 39(XP11.3) WILD-TYPE"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-LN-A4A9 
  "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-IG-A4P3                    TCGA-IG-A4QS 
"DEL PEAK 39(XP11.3) WILD-TYPE"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-L5-A4OE                    TCGA-L5-A4OF 
  "DEL PEAK 39(XP11.3) MUTATED"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-L5-A4OM                    TCGA-L5-A4ON 
  "DEL PEAK 39(XP11.3) MUTATED"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-L5-A4OO                    TCGA-L5-A4OQ 
"DEL PEAK 39(XP11.3) WILD-TYPE" "DEL PEAK 39(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OR                    TCGA-L5-A4OS 
"DEL PEAK 39(XP11.3) WILD-TYPE" "DEL PEAK 39(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OU                    TCGA-L5-A4OW 
"DEL PEAK 39(XP11.3) WILD-TYPE" "DEL PEAK 39(XP11.3) WILD-TYPE" 
                   TCGA-L5-A4OX                    TCGA-LN-A4A2 
"DEL PEAK 39(XP11.3) WILD-TYPE"   "DEL PEAK 39(XP11.3) MUTATED" 
                   TCGA-LN-A4A9 
  "DEL PEAK 39(XP11.3) MUTATED" 
[1] "hr=" "1.8"
D62V2, continuous
                               vv
clus                            STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 39(XP11.3) MUTATED          1         2         3          2
  DEL PEAK 39(XP11.3) WILD-TYPE        1         1         4          2
                               vv
clus                            STAGE IIIB STAGE IIIC
  DEL PEAK 39(XP11.3) MUTATED            2          0
  DEL PEAK 39(XP11.3) WILD-TYPE          0          1
D62V3, multiclass
                               vv
clus                            T1 T2 T3+T4
  DEL PEAK 39(XP11.3) MUTATED    3  2     5
  DEL PEAK 39(XP11.3) WILD-TYPE  1  5     3
D62V4, multiclass
       clus
vv      DEL PEAK 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE
  T1                              3                             1
  T2                              2                             5
  T3+T4                           5                             3
                               vv
clus                            N0 N1+N2+N3
  DEL PEAK 39(XP11.3) MUTATED    5        5
  DEL PEAK 39(XP11.3) WILD-TYPE  2        7
D62V5, multiclass
          clus
vv         DEL PEAK 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE
  N0                                 5                             2
  N1+N2+N3                           5                             7
D62V6, binary
                               cls
clus                            0 1
  DEL PEAK 39(XP11.3) MUTATED   1 9
  DEL PEAK 39(XP11.3) WILD-TYPE 2 7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 39(XP11.3) MUTATED      1    9
  DEL PEAK 39(XP11.3) WILD-TYPE    2    7
        clus
vv       DEL PEAK 39(XP11.3) MUTATED DEL PEAK 39(XP11.3) WILD-TYPE
  FEMALE                           1                             2
  MALE                             9                             7
D62V7, continuous

Clustering(63) Variable = DEL PEAK 40(XQ21.33) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                            0 1
  DEL PEAK 40(XQ21.33) MUTATED   3 1
  DEL PEAK 40(XQ21.33) WILD-TYPE 7 4
  DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE 
                             4                             11 
  DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE 
                             1                              4 
$`DEL PEAK 40(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 40(XQ21.33) WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO 
        0.03         0.26         3.48         3.68        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        30.71        29.00         7.10         7.43 

  DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE 
                          4.08                          30.71 
  DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE 
                         1.645                          3.680 
[1] "0.1 - 4.1 (1.6)"  "0.0 - 30.7 (3.7)"
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 40(XQ21.33) MUTATED" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 40(XQ21.33) MUTATED" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 40(XQ21.33) WILD-TYPE"   "DEL PEAK 40(XQ21.33) MUTATED" 
                    TCGA-LN-A4A9 
  "DEL PEAK 40(XQ21.33) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 40(XQ21.33) MUTATED" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 40(XQ21.33) MUTATED" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 40(XQ21.33) WILD-TYPE"   "DEL PEAK 40(XQ21.33) MUTATED" 
                    TCGA-LN-A4A9 
  "DEL PEAK 40(XQ21.33) MUTATED" 
                    TCGA-IG-A4P3                     TCGA-IG-A4QS 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OE                     TCGA-L5-A4OF 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OM                     TCGA-L5-A4ON 
  "DEL PEAK 40(XQ21.33) MUTATED" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OO                     TCGA-L5-A4OQ 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OR                     TCGA-L5-A4OS 
  "DEL PEAK 40(XQ21.33) MUTATED" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OU                     TCGA-L5-A4OW 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OX                     TCGA-LN-A4A2 
"DEL PEAK 40(XQ21.33) WILD-TYPE"   "DEL PEAK 40(XQ21.33) MUTATED" 
                    TCGA-LN-A4A9 
  "DEL PEAK 40(XQ21.33) MUTATED" 
[1] "hr=" "4.2"
D63V2, continuous
                                vv
clus                             STAGE IA STAGE IIA STAGE IIB STAGE IIIA
  DEL PEAK 40(XQ21.33) MUTATED          2         2         0          0
  DEL PEAK 40(XQ21.33) WILD-TYPE        0         1         7          4
                                vv
clus                             STAGE IIIB STAGE IIIC
  DEL PEAK 40(XQ21.33) MUTATED            0          0
  DEL PEAK 40(XQ21.33) WILD-TYPE          2          1
D63V3, multiclass
                                vv
clus                             T1 T2 T3+T4
  DEL PEAK 40(XQ21.33) MUTATED    2  1     1
  DEL PEAK 40(XQ21.33) WILD-TYPE  2  6     7
D63V4, multiclass
       clus
vv      DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE
  T1                               2                              2
  T2                               1                              6
  T3+T4                            1                              7
                                vv
clus                             N0 N1+N2+N3
  DEL PEAK 40(XQ21.33) MUTATED    4        0
  DEL PEAK 40(XQ21.33) WILD-TYPE  3       12
D63V5, multiclass
          clus
vv         DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE
  N0                                  4                              3
  N1+N2+N3                            0                             12
D63V6, binary
                                cls
clus                              0  1
  DEL PEAK 40(XQ21.33) MUTATED    1  3
  DEL PEAK 40(XQ21.33) WILD-TYPE  2 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(XQ21.33) MUTATED      1    3
  DEL PEAK 40(XQ21.33) WILD-TYPE    2   13
        clus
vv       DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE
  FEMALE                            1                              2
  MALE                              3                             13
D63V7, continuous
[1] "Remove cluster labels:"       "DEL PEAK 40(XQ21.33) MUTATED"
clus
  DEL PEAK 40(XQ21.33) MUTATED DEL PEAK 40(XQ21.33) WILD-TYPE 
                             2                             10 
                    TCGA-IG-A3Y9                     TCGA-IG-A3YA 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-IG-A4P3                     TCGA-L5-A4OE 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4ON                     TCGA-L5-A4OO 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OQ                     TCGA-L5-A4OU 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
                    TCGA-L5-A4OW                     TCGA-L5-A4OX 
"DEL PEAK 40(XQ21.33) WILD-TYPE" "DEL PEAK 40(XQ21.33) WILD-TYPE" 
> q(save="no")
