[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTSKCM-TM"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/10006254/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/10013811/transformed.cor.cli.txt"

nPatients in clinical file=295, in cluster file=299, common to both=281
[1]  54 281
[1] "AMP PEAK  1(1P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         89                         192 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         89                         192 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          148                           133 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          148                           133 
[1] "AMP PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        152                         129 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        152                         129 
[1] "AMP PEAK  4(3P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         76                         205 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         76                         205 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         52                         229 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         52                         229 
[1] "AMP PEAK  6(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            89                            192 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            89                            192 
[1] "AMP PEAK  7(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           47                           234 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           47                           234 
[1] "AMP PEAK  8(6P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          159                           122 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          159                           122 
[1] "AMP PEAK  9(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         63                         218 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         63                         218 
[1] "AMP PEAK 10(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          155                           126 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          155                           126 
[1] "AMP PEAK 11(7Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        169                         112 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        169                         112 
[1] "AMP PEAK 12(8Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                           127                            154 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                           127                            154 
[1] "AMP PEAK 13(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           146                            135 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           146                            135 
[1] "AMP PEAK 14(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            54                            227 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            54                            227 
[1] "AMP PEAK 15(11Q13.4) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                            50                            231 
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                            50                            231 
[1] "AMP PEAK 16(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                            50                            231 
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                            50                            231 
[1] "AMP PEAK 17(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          48                          233 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          48                          233 
[1] "AMP PEAK 18(13Q12.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                            80                            201 
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                            80                            201 
[1] "AMP PEAK 19(15Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                            93                            188 
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                            93                            188 
[1] "AMP PEAK 20(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                            96                            185 
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                            96                            185 
[1] "AMP PEAK 21(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            53                            228 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            53                            228 
[1] "AMP PEAK 22(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                            147                             134 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                            147                             134 
[1] "AMP PEAK 23(22Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                           122                            159 
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                           122                            159 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            68                            213 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            68                            213 
[1] "DEL PEAK  2(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           71                           210 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           71                           210 
[1] "DEL PEAK  3(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           69                           212 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           69                           212 
[1] "DEL PEAK  4(3P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                           54                           227 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                           54                           227 
[1] "DEL PEAK  5(3Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                         46                         235 
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                         46                         235 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           78                           203 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           78                           203 
[1] "DEL PEAK  7(5P15.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                            59                            222 
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                            59                            222 
[1] "DEL PEAK  8(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           77                           204 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           77                           204 
[1] "DEL PEAK  9(5Q31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                          106                           175 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                          106                           175 
[1] "DEL PEAK 10(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                           169                            112 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                           169                            112 
[1] "DEL PEAK 11(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        174                         107 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        174                         107 
[1] "DEL PEAK 12(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                           65                           216 
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                           65                           216 
[1] "DEL PEAK 13(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                        191                          90 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                        191                          90 
[1] "DEL PEAK 14(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          214                            67 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          214                            67 
[1] "DEL PEAK 15(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                           154                            127 
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                           154                            127 
[1] "DEL PEAK 16(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                            175                             106 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                            175                             106 
[1] "DEL PEAK 17(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                           180                            101 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                           180                            101 
[1] "DEL PEAK 18(11P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                            91                            190 
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                            91                            190 
[1] "DEL PEAK 19(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                           154                            127 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                           154                            127 
[1] "DEL PEAK 20(12Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                            68                            213 
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                            68                            213 
[1] "DEL PEAK 21(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             65                             216 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             65                             216 
[1] "DEL PEAK 22(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                          62                          219 
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                          62                          219 
[1] "DEL PEAK 23(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                            96                            185 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                            96                            185 
[1] "DEL PEAK 24(14Q32.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                            95                            186 
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                            95                            186 
[1] "DEL PEAK 25(15Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                            69                            212 
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                            69                            212 
[1] "DEL PEAK 26(15Q14) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                          70                          211 
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                          70                          211 
[1] "DEL PEAK 27(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                            73                            208 
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                            73                            208 
[1] "DEL PEAK 28(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            53                            228 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            53                            228 
[1] "DEL PEAK 29(16Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            92                            189 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            92                            189 
[1] "DEL PEAK 30(16Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                           101                            180 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                           101                            180 
[1] "DEL PEAK 31(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            81                            200 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            81                            200 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DAYSTOSUBMITTEDSPECIMENDX"             
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "NEOPLASM.DISEASESTAGE"                 
 [8] "PATHOLOGY.T.STAGE"                     
 [9] "PATHOLOGY.N.STAGE"                     
[10] "PATHOLOGY.M.STAGE"                     
[11] "MELANOMA.ULCERATION"                   
[12] "MELANOMA.PRIMARY.KNOWN"                
[13] "BRESLOW.THICKNESS"                     
[14] "DCCUPLOADDATE"                         
[15] "GENDER"                                
[16] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[17] "RADIATIONTHERAPY"                      
[18] "RADIATIONS.RADIATION.REGIMENINDICATION"
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 281 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
          NA           NA         3408           NA           NA         4053 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
          NA           NA         2765         2912           NA           NA 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
          NA           NA         3514           NA         2126           NA 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
        1483           NA         1280           NA         5219         1709 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 
        2010         1372         3976           NA           NA           NA 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
        1429         1409         5065         2644           NA           NA 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
          NA           NA         3151         1209          653         4923 
TCGA-D3-A51F TCGA-D3-A51G TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
        1329           NA         1221         4012          559          305 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        1572          458         3374         4129         4195         5055 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
         226         3808         4609         1663          111          195 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
         345           99          301          766         2015           NA 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        1487           NA         3565           NA         5926           NA 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
          NA         3265         1861           NA           NA          713 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
          NA          870           NA         6553          477          422 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
         309          543         1372         1065          108         1582 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
         193          371           NA           NA           NA           NA 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
          NA           NA           NA           NA           NA         3335 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
          NA         2399           NA           NA           NA         2452 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        1455           NA         1205           NA          979           NA 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1349           NA         1716         1136          440         1701 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       10523           NA         5218           NA           NA         3130 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
         743           NA         1787         1446         2051         9568 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
        4135         6328         1482         2717         1665         2423 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
        2296         2767         3101           NA          435         1691 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        1365         2884           NA         3932           NA           NA 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
          NA         4403         6176           NA           NA         7563 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
          NA         3150         4151         1265         1620         3781 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
        3733          786          112         1658           NA          714 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
          NA           NA           NA           NA         1949           NA 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
          NA           NA         1016         3096         4504           NA 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
          NA           NA           NA           NA         2365           NA 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
          NA           NA           NA           NA         8180           NA 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A19P 
          NA           NA           NA         1340           NA           NA 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
          NA         1133           NA         2433           NA           NA 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
          NA          498          951          975           NA         2443 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FR-A69P 
        1429         1010         2828           NA         5299          149 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        6390          461          213           NA           NA           NA 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
          NA           NA         1225           NA           NA           NA 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
          NA           NA         3080           NA           NA           NA 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        4526         1617           NA         1505           NA           NA 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        2367           NA           NA           NA           NA          378 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
          NA         1504         2369            6          697         1446 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
           5           73          301          220          427         3664 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
          NA         2577           NA           NA           NA           NA 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
        1204         1410          384         8966          203 
Variable 1:'AGE':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=133,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=148,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=222,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'NEOPLASM.DISEASESTAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.T.STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.N.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA.ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MELANOMA.PRIMARY.KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BRESLOW.THICKNESS':	nDistinctValues=112,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
 [3] "NEOPLASM.DISEASESTAGE"   "PATHOLOGY.T.STAGE"      
 [5] "PATHOLOGY.N.STAGE"       "PATHOLOGY.M.STAGE"      
 [7] "MELANOMA.ULCERATION"     "MELANOMA.PRIMARY.KNOWN" 
 [9] "BRESLOW.THICKNESS"       "GENDER"                 
[11] "RACE"                    "ETHNICITY"              
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 281 columns, 2 survival variables, and 12 non-survival variables.
AGE, nv=66, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
NEOPLASM.DISEASESTAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
22 31 60 55 57 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   53    60    55    57 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
22 31 60 55 57 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   53    60    55    57 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
141  51  32  37 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
141  51  32  37 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
141  51  32  37 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
141  51  32  37 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
MELANOMA.ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA.PRIMARY.KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW.THICKNESS, nv=112, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P12) MUTATION ANALYSIS
D1V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  1(1P12) MUTATED   40 46
  AMP PEAK  1(1P12) WILD-TYPE 97 87
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         86                         184 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         46                          87 
$`AMP PEAK  1(1P12) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       16.47         8.52        10.29        88.50        69.90        11.41 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MO 
       92.42        64.44       114.67        15.25         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A3Z1 
      103.59        80.22        20.48        47.87         6.97         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-EB-A44R 
        2.89         9.90        11.31        13.22         7.00         0.20 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       13.22         0.20         8.12         1.12        12.20         4.31 
TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       36.07         1.18        37.97        11.15        38.63         8.55 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB 
        1.08        27.12         2.43         8.68         8.09        39.39 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MD 
       30.08        19.43        35.54         5.42         1.15         9.53 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU 
       14.56        63.42        56.02        21.60        29.65         5.56 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
      122.73         3.68        15.95         3.22        21.60        22.22 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A2ND 
        5.72         3.52        11.90       114.15        13.45         1.87 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        6.58         1.71        18.41        85.74         4.90         6.71 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZU 
        5.36         3.45        30.87        12.89         8.65         8.68 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A266 
        3.22        28.73         0.20         7.23        31.33        10.13 
TCGA-GN-A267 TCGA-GN-A26A 
       16.24        12.16 

$`AMP PEAK  1(1P12) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      111.09        32.42        70.16       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       45.83        81.24        85.32         8.38        21.14        68.22 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP 
       30.87         7.50        36.16         6.31        56.19        45.11 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37         5.39        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
        8.84        13.94        95.38        52.01         1.55        23.11 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       14.60        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36        17.56        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.13         0.00         0.00        11.57        10.55         6.31 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        1.35         5.13         4.34         5.13         9.21         7.99 
TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        9.90         4.41         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         6.48        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
        8.94        34.29        17.98        34.92        47.21        16.01 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       28.31        33.83        30.84        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
        8.84        98.27         2.70         6.18        47.51        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       44.25         7.96       111.78       111.91        25.08        26.99 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       27.16        23.05       124.31        25.84        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       12.72        22.92        21.60        16.14        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       76.41        25.18         3.78        11.11        34.88         4.21 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44        11.80         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        9.04        22.49         3.58        64.47        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
        8.22        19.53        11.08         7.17        12.92        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       52.08         8.81        49.15        40.64        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23        53.85         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
        9.90        12.85        24.85        84.72        15.42        14.70 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                        0.2                         0.0 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                     122.73                      124.31 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                     11.360                      15.765 
[1] "0.2 - 122.7 (11.4)" "0.0 - 124.3 (15.8)"
[1] "hr=" "1.3"
D1V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  1(1P12) MUTATED    41  46
  AMP PEAK  1(1P12) WILD-TYPE 101  88
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         87                         189 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         46                          88 
$`AMP PEAK  1(1P12) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       16.57        16.67        43.43       115.53        69.90        11.87 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MO 
      171.58        66.08       130.72        58.06        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A3Z1 
      103.59       161.85        51.68       137.92         7.43        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-EB-A44R 
        3.25         9.90        25.18        66.25        10.49        10.16 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
        3.55        52.01        12.20        94.98        33.73        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.96       109.64        13.55        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       72.07         2.60        44.35        25.87       171.55        17.92 
TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR 
       47.54        48.72        89.33        79.66        13.91        14.30 
TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR 
       47.28       204.66        96.23       167.90        43.23       103.56 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 
       53.26       122.73         3.68        23.47       172.18        64.08 
TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L 
       53.19         9.17        12.59        13.02       268.93       131.51 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       23.34        80.32        33.21        92.98       174.21         4.90 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZQ 
      210.08         7.00        48.59        32.75        23.93       133.55 
TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GN-A264 
       26.56        50.14        28.73         0.20         7.23       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       10.13        64.44        32.48 

$`AMP PEAK  1(1P12) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        95.74       103.10        65.49        23.77       168.00 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP 
       48.76       113.52        42.08        12.10        56.19        45.11 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75        21.47        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU 
       10.03        15.06       110.93       135.75       166.19       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A6EG TCGA-DA-A1HV 
      151.53        54.67         3.65         6.41        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       28.60       215.44        15.68        13.87        17.85        45.11 
TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
       35.01         6.35        29.82        27.22         8.65        14.70 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
       68.15       151.27        78.87       168.26        63.35        80.61 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       32.19        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
      345.96        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GM 
       67.43       314.56       135.95       208.04        54.74        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97       101.95        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
      129.27        28.83        19.76        61.51       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
       16.96       144.76       203.05        47.54       248.65       136.47 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
       41.59       124.31        25.84        54.51        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        36.95        34.32        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
      148.08        31.40        35.44        13.94        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       98.40        48.89        26.37       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       46.98        15.16       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       40.27        15.45         9.70        47.38       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        53.16        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 
       14.04       120.46        84.72        62.79        39.58        46.36 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                       0.20                        0.16 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                     268.93                      357.37 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                      43.43                       48.89 
[1] "0.2 - 268.9 (43.4)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.4"
D1V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  1(1P12) MUTATED                    9             3
  AMP PEAK  1(1P12) WILD-TYPE                 28             1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  1(1P12) MUTATED                                          23
  AMP PEAK  1(1P12) WILD-TYPE                                        37
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  1(1P12) MUTATED                    54
  AMP PEAK  1(1P12) WILD-TYPE                 125
D1V4, multiclass
                                           clus
vv                                          AMP PEAK  1(1P12) MUTATED
  DISTANT METASTASIS                                                9
  PRIMARY TUMOR                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        23
  REGIONAL LYMPH NODE                                              54
                                           clus
vv                                          AMP PEAK  1(1P12) WILD-TYPE
  DISTANT METASTASIS                                                 28
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          37
  REGIONAL LYMPH NODE                                               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  1(1P12) MUTATED             4       3       5        3       10
  AMP PEAK  1(1P12) WILD-TYPE           6       3      18        7       15
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  1(1P12) MUTATED          7         2         3         4         9
  AMP PEAK  1(1P12) WILD-TYPE       10         8        11         6        23
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  1(1P12) MUTATED            9          6         14        5
  AMP PEAK  1(1P12) WILD-TYPE          5         17         34        7
D1V5, multiclass
             clus
vv            AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  I OR II NOS                         4                           6
  STAGE 0                             3                           3
  STAGE I                             5                          18
  STAGE IA                            3                           7
  STAGE IB                           10                          15
  STAGE II                            7                          10
  STAGE IIA                           2                           8
  STAGE IIB                           3                          11
  STAGE IIC                           4                           6
  STAGE III                           9                          23
  STAGE IIIA                          9                           5
  STAGE IIIB                          6                          17
  STAGE IIIC                         14                          34
  STAGE IV                            5                           7
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  1(1P12) MUTATED      13 18 20 20
  AMP PEAK  1(1P12) WILD-TYPE    40 42 35 37
D1V6, multiclass
       clus
vv      AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  T0+T1                        13                          40
  T2                           18                          42
  T3                           20                          35
  T4                           20                          37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  AMP PEAK  1(1P12) MUTATED   46 17 10 11
  AMP PEAK  1(1P12) WILD-TYPE 95 34 22 26
D1V7, multiclass
    clus
vv   AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  N0                        46                          95
  N1                        17                          34
  N2                        10                          22
  N3                        11                          26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  AMP PEAK  1(1P12) MUTATED    79   1   1   0   3
  AMP PEAK  1(1P12) WILD-TYPE 173   3   1   2   2
D1V8, multiclass
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  M0                         79                         173
  M1                          1                           3
  M1A                         1                           1
  M1B                         0                           2
  M1C                         3                           2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                             cls
clus                           0  1
  AMP PEAK  1(1P12) MUTATED   37 21
  AMP PEAK  1(1P12) WILD-TYPE 67 51
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     37   21
  AMP PEAK  1(1P12) WILD-TYPE   67   51
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  NO                         37                          67
  YES                        21                          51
[1] 2 2
[1] FALSE
D1V10, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED    10  79
  AMP PEAK  1(1P12) WILD-TYPE  24 168
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     10   79
  AMP PEAK  1(1P12) WILD-TYPE   24  168
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  NO                         10                          24
  YES                        79                         168
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED    35  54
  AMP PEAK  1(1P12) WILD-TYPE  73 119
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     35   54
  AMP PEAK  1(1P12) WILD-TYPE   73  119
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  FEMALE                        35                          73
  MALE                          54                         119
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P12) MUTATED       2                         0    87
  AMP PEAK  1(1P12) WILD-TYPE     3                         1   188
D1V13, multiclass
                           clus
vv                          AMP PEAK  1(1P12) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            87
                           clus
vv                          AMP PEAK  1(1P12) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED     1  88
  AMP PEAK  1(1P12) WILD-TYPE   2 186
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      1   88
  AMP PEAK  1(1P12) WILD-TYPE    2  186
                        clus
vv                       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  HISPANIC OR LATINO                             1                           2
  NOT HISPANIC OR LATINO                        88                         186
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   75 69
  AMP PEAK  2(1Q21.3) WILD-TYPE 62 64
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          144                           126 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           69                            64 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 
       16.47         8.52       110.79        28.08        81.24         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       21.14        88.50        69.90        11.41        92.42        56.19 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      114.67        15.25        13.32         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       26.37         5.39        80.22        17.72        20.48        52.01 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       47.87         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       11.31        13.22        14.60        10.03        39.19         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 
       44.52        36.69         4.93         6.64         7.00        17.56 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
        0.20         0.00        13.22         0.20        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       36.07         9.21         1.18         9.90        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        8.55         1.08        27.12         8.84         9.99         6.48 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
        8.68        49.22        23.90         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        47.21        30.08        19.43        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MJ 
       33.83        30.84        13.02        36.33         2.70        63.42 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
      122.73        25.84         3.68        15.95         3.22        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D 
       21.60        22.22        13.94        12.95         5.72         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND 
       11.90        11.11       114.15        34.88         9.57         1.87 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       12.62        22.49         1.71        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        6.71         5.36        64.47         3.45        23.80        14.24 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZK 
        7.30        20.38         8.22        11.08        30.87        12.89 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       52.08         8.65        40.64         8.68         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A6C8 TCGA-GN-A266 
       53.85        28.73         2.27         0.20        12.85        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       16.24        12.16        14.70        11.84        10.65         5.79 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
      111.09        32.42        70.16        22.55        45.83        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       85.32        68.22        30.87         7.50        36.16         6.31 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.44        45.11        46.98        46.32        82.29        61.38 
TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T 
       24.00        42.71        15.09        41.10         8.84        13.94 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
       95.38         1.55        48.79        35.80        51.12        13.68 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       25.15        22.36        19.36        14.83        13.15         0.13 
TCGA-EB-A5SG TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
        0.00        11.57         4.34         5.13         7.99        37.97 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X 
        4.41         9.50        12.03         8.09         2.43         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GP TCGA-EE-A2GR 
       11.31         9.67        34.29        16.01         5.42         1.15 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       34.98         8.84        98.27         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
       56.02        26.99       124.31        30.15        13.81        12.72 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 
       22.92        16.14        27.35         0.46        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19J 
       18.61        38.40        76.41        25.18         3.78         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W 
       13.45        28.60        42.84        34.68        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       78.44        11.80         1.51        13.08        11.74         9.04 
TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
        6.58         3.58        11.01        15.52         7.33         3.39 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       19.53         7.17        12.92        47.38         8.81        49.15 
TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.39         3.22         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-OD-A75X 
        7.23        24.85        31.33        84.72        15.42        11.05 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                            0                             0 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       122.73                        124.31 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       13.120                        15.255 
[1] "0.0 - 122.7 (13.1)" "0.0 - 124.3 (15.3)"
[1] "hr=" "1"  
D2V2, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   77 70
  AMP PEAK  2(1Q21.3) WILD-TYPE 65 64
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          147                           129 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           70                            64 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 
       16.57        16.67       133.25        28.08        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       23.77       115.53        69.90        11.87       171.58        56.19 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      130.72        58.06        60.23        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       39.75        21.47       161.85        18.38        51.68       135.75 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      137.92         7.43       125.19         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 
        3.25         9.90        25.18        66.25        22.95        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      194.83        35.93       107.34        61.18        65.92        68.09 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.49       215.44        10.16        35.01         3.55        52.01 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       12.20        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I 
       26.89        68.15         4.96       109.64       168.26        13.55 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M 
       80.61        13.97        39.62        72.07         2.60        44.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        55.92       345.96       171.55       102.90        24.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       58.75        47.54       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS 
       89.33        79.66        75.48        90.97       101.95        55.59 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       94.82        28.83        96.23        47.54        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        41.59        53.26       122.73        25.84         3.68 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH 
       23.47       172.18        36.95        64.08        53.19       101.79 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       13.94         9.17        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL 
      152.35        50.89        23.34        31.27        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW 
       92.98       174.21         4.90       210.08         7.00       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
       48.59       202.65        20.91        27.72       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       15.45        32.75        23.93        74.73       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FD 
       26.56        27.09        27.02        77.82        28.73        77.88 
TCGA-FW-A3I3 TCGA-GF-A6C8 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20        14.04        10.13        64.44        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       46.36        12.62         6.67 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
      112.04       112.57        71.80        31.59        90.90        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      103.10       168.00        48.76       113.52        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.08        45.11        46.98        46.32       166.52        86.93 
TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T 
       24.53        43.69        40.14       131.90        10.03        15.06 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D9-A148 TCGA-D9-A149 TCGA-DA-A1HV TCGA-DA-A1HW 
      110.93       166.19       151.53        54.67        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
      117.21       176.55        53.92        23.44        28.60        15.68 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A20C 
       13.87        17.85        45.11         6.35        29.82       151.27 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       78.87        63.35        47.84        32.19        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC 
       37.35        25.87        17.92        46.82        39.29        67.43 
TCGA-EE-A2GK TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       54.74        13.91        14.30        44.88        21.67       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA 
      204.66       144.76       203.05       167.90       248.65       124.31 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD 
       54.51        13.81       138.81       127.20        34.32        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       33.40       148.08        31.40        35.44        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       98.40        48.89         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      162.08        37.25       148.18        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YY 
       16.37        32.05       247.04        80.32        15.16       228.59 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       28.08         7.79        48.85        40.27         9.70        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 
      101.26        11.41       148.80        49.48        50.14        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
      174.84        12.43        26.73        49.45        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 
        0.16         2.40         9.90         7.23       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-OD-A75X 
       84.72        62.79       294.77 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.20                          0.16 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       357.37                        294.77 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        47.54                         48.76 
[1] "0.2 - 357.4 (47.5)" "0.2 - 294.8 (48.8)"
[1] "hr=" "1"  
D2V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  2(1Q21.3) MUTATED                   23             3
  AMP PEAK  2(1Q21.3) WILD-TYPE                 14             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  2(1Q21.3) MUTATED                                          33
  AMP PEAK  2(1Q21.3) WILD-TYPE                                        27
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK  2(1Q21.3) MUTATED                    88
  AMP PEAK  2(1Q21.3) WILD-TYPE                  91
D2V4, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  DISTANT METASTASIS                                                 23
  PRIMARY TUMOR                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          33
  REGIONAL LYMPH NODE                                                88
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  DISTANT METASTASIS                                                   14
  PRIMARY TUMOR                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            27
  REGIONAL LYMPH NODE                                                  91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  2(1Q21.3) MUTATED             4       3       9        6       17
  AMP PEAK  2(1Q21.3) WILD-TYPE           6       3      14        4        8
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  2(1Q21.3) MUTATED          9         5         8         6
  AMP PEAK  2(1Q21.3) WILD-TYPE        8         5         6         4
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  2(1Q21.3) MUTATED          17         10         13         23
  AMP PEAK  2(1Q21.3) WILD-TYPE        15          4         10         25
                               vv
clus                            STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED          9
  AMP PEAK  2(1Q21.3) WILD-TYPE        3
D2V5, multiclass
             clus
vv            AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  I OR II NOS                           4                             6
  STAGE 0                               3                             3
  STAGE I                               9                            14
  STAGE IA                              6                             4
  STAGE IB                             17                             8
  STAGE II                              9                             8
  STAGE IIA                             5                             5
  STAGE IIB                             8                             6
  STAGE IIC                             6                             4
  STAGE III                            17                            15
  STAGE IIIA                           10                             4
  STAGE IIIB                           13                            10
  STAGE IIIC                           23                            25
  STAGE IV                              9                             3
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  2(1Q21.3) MUTATED      31 32 31 32
  AMP PEAK  2(1Q21.3) WILD-TYPE    22 28 24 25
D2V6, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T0+T1                          31                            22
  T2                             32                            28
  T3                             31                            24
  T4                             32                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  2(1Q21.3) MUTATED   78 25 20 19
  AMP PEAK  2(1Q21.3) WILD-TYPE 63 26 12 18
D2V7, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          78                            63
  N1                          25                            26
  N2                          20                            12
  N3                          19                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  AMP PEAK  2(1Q21.3) MUTATED   135   2   2   1   4
  AMP PEAK  2(1Q21.3) WILD-TYPE 117   2   0   1   1
D2V8, multiclass
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  M0                          135                           117
  M1                            2                             2
  M1A                           2                             0
  M1B                           1                             1
  M1C                           4                             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   60 39
  AMP PEAK  2(1Q21.3) WILD-TYPE 44 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     60   39
  AMP PEAK  2(1Q21.3) WILD-TYPE   44   33
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           60                            44
  YES                          39                            33
[1] 2 2
[1] FALSE
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    18 130
  AMP PEAK  2(1Q21.3) WILD-TYPE  16 117
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     18  130
  AMP PEAK  2(1Q21.3) WILD-TYPE   16  117
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           18                            16
  YES                         130                           117
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   58 90
  AMP PEAK  2(1Q21.3) WILD-TYPE 50 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     58   90
  AMP PEAK  2(1Q21.3) WILD-TYPE   50   83
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          58                            50
  MALE                            90                            83
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q21.3) MUTATED       3                         0   145
  AMP PEAK  2(1Q21.3) WILD-TYPE     2                         1   130
D2V13, multiclass
                           clus
vv                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             145
                           clus
vv                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     3 144
  AMP PEAK  2(1Q21.3) WILD-TYPE   0 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      3  144
  AMP PEAK  2(1Q21.3) WILD-TYPE    0  130
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         144
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                           130
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q44) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  3(1Q44) MUTATED   80 68
  AMP PEAK  3(1Q44) WILD-TYPE 57 65
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        148                         122 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         68                          65 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 
       16.47         8.52       110.79        28.08        81.24         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       21.14        88.50        69.90        11.41        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3ML 
       64.44       114.67        15.25        46.98        13.32         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K 
        9.34       103.59        26.37         5.39        80.22        17.72 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       20.48        95.38        52.01        47.87         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01         2.89         9.90        11.31        13.22        14.60 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        39.19         9.99        44.52        36.69 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH 
        4.93         6.64         7.00        17.56         0.20         0.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       13.22         0.20        10.55         8.12         1.12         1.35 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B 
        5.13         4.31        36.07         9.21         1.18         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       11.15        38.63         8.55         1.08        27.12        12.03 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        8.84         6.48         8.68        49.22        23.90         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.39        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       28.31        33.83        30.84        13.02        36.33         2.70 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       63.42       111.91        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16        23.05         5.56       122.73        25.84         3.68 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH 
       15.95        12.72         3.22        21.60        22.22        13.94 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       12.95         5.72         3.78         3.52        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH 
       34.88        34.68         9.57         1.87        13.08        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC 
        4.90         6.71         3.45        23.80        14.24        20.38 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       11.08        30.87        12.92        12.89        52.08         8.65 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 
       40.64         8.68         0.82         5.23        53.85        28.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        6.41         2.27         0.20        10.13        16.24        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       14.70        11.84        10.65         5.79 

$`AMP PEAK  3(1Q44) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
      111.09        32.42        70.16        22.55        45.83        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       85.32        68.22        30.87         7.50        36.16         6.31 
TCGA-D3-A2JP TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51F 
       45.11        46.32        82.29        61.38        24.00        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GR TCGA-DA-A1HV 
       15.09        41.10         8.84        13.94         1.55        48.79 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
       35.80        13.68        25.15        22.36        19.36        14.83 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 
       13.15         0.13         0.00        11.57         6.31        12.20 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N 
        4.34         5.13         7.99        37.97         4.41         9.50 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 
        8.09         9.99         2.43         8.09        11.31         9.67 
TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       34.29        16.01        35.54         5.42         1.15        34.98 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
        8.84        98.27         6.18        47.51         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A3AA 
       44.25         7.96        14.56       111.78        56.02       124.31 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD 
       30.15        13.81        22.92        21.60        16.14        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
        0.46        33.60        31.40        18.61        38.40        76.41 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       25.18        11.90         4.21        13.45        28.60        42.84 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       36.07        17.72        78.44        11.80         1.51        12.62 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.58         5.36        64.47        11.01        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
        7.30         3.39         8.22        19.53         7.17        47.38 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
        8.81        49.15        27.39         3.22         7.36        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       10.78         5.98         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A268 TCGA-OD-A75X 
       15.42        11.05 

  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                          0                           0 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     122.73                      124.31 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     13.270                      14.695 
[1] "0.0 - 122.7 (13.3)" "0.0 - 124.3 (14.7)"
[1] "hr=" "1.1"
D3V2, survival
                             sevent
clus2                          0  1
  AMP PEAK  3(1Q44) MUTATED   82 69
  AMP PEAK  3(1Q44) WILD-TYPE 60 65
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        151                         125 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         69                          65 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 
       16.57        16.67       133.25        28.08        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       23.77       115.53        69.90        11.87       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3ML 
       66.08       130.72        58.06        46.98        60.23        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K 
        9.34       103.59        39.75        21.47       161.85        18.38 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       51.68       110.93       135.75       137.92         7.43       125.19 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       66.25        22.95       117.21        20.38       194.83        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 
      107.34        61.18        65.92        68.09        10.49       215.44 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y 
       10.16        35.01         3.55        52.01        12.20        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        33.73        14.70        68.15         4.96       109.64 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
      168.26        13.55        80.61        13.97        39.62        72.07 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W 
        2.60        44.35        56.42        14.47       345.96       171.55 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        24.43        58.75        47.54       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      208.04        48.72        89.33        75.48        90.97       101.95 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
       55.59        94.82        28.83        96.23       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       103.56       136.47        41.59        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        25.84         3.68        23.47       138.81       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       64.08        53.19       101.79        13.94         9.17        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19Q 
       12.59        26.37       268.93       152.35       162.08        50.89 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       23.34        16.37        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       210.08        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      202.65        20.91       357.37        15.45        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
       23.93        74.73       133.55        53.16        26.56        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       27.02        77.82        28.73        49.45        77.88         0.20 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        64.44        32.48        39.58        46.36        12.62 
TCGA-QB-A6FS 
        6.67 

$`AMP PEAK  3(1Q44) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
      112.04       112.57        71.80        31.59        90.90        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      103.10       168.00        48.76       113.52        42.08        12.10 
TCGA-D3-A2JP TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51F 
       45.11        46.32       166.52        86.93        24.53        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GR TCGA-D9-A148 
       40.14       131.90        10.03        15.06       166.19       151.53 
TCGA-D9-A149 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB 
       54.67        48.89        36.03       176.55        53.92        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV 
       28.60        15.68        13.87        17.85        45.11         6.35 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A 
       29.82         8.65        26.89       151.27        78.87        63.35 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       47.84        32.19        18.61        37.35        55.92        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL 
       17.92        46.82        39.29        67.43        54.74        79.66 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
       13.91        14.30        44.88        21.67       129.27        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      144.76       167.90       124.31        54.51        13.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 
       36.95        34.32        27.35        33.40       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19J 
       35.44        50.76        77.75        98.40        13.02         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
      131.51        61.05        44.05        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       43.82        20.15        31.27        15.16         7.00       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
      228.59        28.08         7.79        27.72        48.85        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW 
       40.27         9.70       101.26        11.41       148.80        49.48 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3R5 
       50.14        66.67       174.84        12.43        26.73        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-OD-A75X 
      120.46       117.93        84.72        62.79       294.77 

  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                       0.20                        0.16 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     357.37                      294.77 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                      50.89                       45.11 
[1] "0.2 - 357.4 (50.9)" "0.2 - 294.8 (45.1)"
[1] "hr=" "1.3"
D3V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  3(1Q44) MUTATED                   23             4
  AMP PEAK  3(1Q44) WILD-TYPE                 14             0
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  3(1Q44) MUTATED                                          35
  AMP PEAK  3(1Q44) WILD-TYPE                                        25
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  3(1Q44) MUTATED                    89
  AMP PEAK  3(1Q44) WILD-TYPE                  90
D3V4, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q44) MUTATED
  DISTANT METASTASIS                                               23
  PRIMARY TUMOR                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        35
  REGIONAL LYMPH NODE                                              89
                                           clus
vv                                          AMP PEAK  3(1Q44) WILD-TYPE
  DISTANT METASTASIS                                                 14
  PRIMARY TUMOR                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          25
  REGIONAL LYMPH NODE                                                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  3(1Q44) MUTATED             4       2      12        6       16
  AMP PEAK  3(1Q44) WILD-TYPE           6       4      11        4        9
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  3(1Q44) MUTATED         11         3         6         7        17
  AMP PEAK  3(1Q44) WILD-TYPE        6         7         8         3        15
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  3(1Q44) MUTATED           11         12         25        9
  AMP PEAK  3(1Q44) WILD-TYPE          3         11         23        3
D3V5, multiclass
             clus
vv            AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  I OR II NOS                         4                           6
  STAGE 0                             2                           4
  STAGE I                            12                          11
  STAGE IA                            6                           4
  STAGE IB                           16                           9
  STAGE II                           11                           6
  STAGE IIA                           3                           7
  STAGE IIB                           6                           8
  STAGE IIC                           7                           3
  STAGE III                          17                          15
  STAGE IIIA                         11                           3
  STAGE IIIB                         12                          11
  STAGE IIIC                         25                          23
  STAGE IV                            9                           3
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  3(1Q44) MUTATED      31 35 30 32
  AMP PEAK  3(1Q44) WILD-TYPE    22 25 25 25
D3V6, multiclass
       clus
vv      AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  T0+T1                        31                          22
  T2                           35                          25
  T3                           30                          25
  T4                           32                          25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  AMP PEAK  3(1Q44) MUTATED   79 26 19 21
  AMP PEAK  3(1Q44) WILD-TYPE 62 25 13 16
D3V7, multiclass
    clus
vv   AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  N0                        79                          62
  N1                        26                          25
  N2                        19                          13
  N3                        21                          16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  AMP PEAK  3(1Q44) MUTATED   138   2   2   1   4
  AMP PEAK  3(1Q44) WILD-TYPE 114   2   0   1   1
D3V8, multiclass
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  M0                        138                         114
  M1                          2                           2
  M1A                         2                           0
  M1B                         1                           1
  M1C                         4                           1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   61 38
  AMP PEAK  3(1Q44) WILD-TYPE 43 34
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     61   38
  AMP PEAK  3(1Q44) WILD-TYPE   43   34
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         61                          43
  YES                        38                          34
[1] 2 2
[1] FALSE
D3V10, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    19 133
  AMP PEAK  3(1Q44) WILD-TYPE  15 114
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     19  133
  AMP PEAK  3(1Q44) WILD-TYPE   15  114
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         19                          15
  YES                       133                         114
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   60 92
  AMP PEAK  3(1Q44) WILD-TYPE 48 81
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     60   92
  AMP PEAK  3(1Q44) WILD-TYPE   48   81
        clus
vv       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  FEMALE                        60                          48
  MALE                          92                          81
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q44) MUTATED       3                         0   149
  AMP PEAK  3(1Q44) WILD-TYPE     2                         1   126
D3V13, multiclass
                           clus
vv                          AMP PEAK  3(1Q44) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                           149
                           clus
vv                          AMP PEAK  3(1Q44) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED     3 148
  AMP PEAK  3(1Q44) WILD-TYPE   0 126
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED      3  148
  AMP PEAK  3(1Q44) WILD-TYPE    0  126
                        clus
vv                       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             3                           0
  NOT HISPANIC OR LATINO                       148                         126
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3P13) MUTATION ANALYSIS
D4V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  4(3P13) MUTATED    48  25
  AMP PEAK  4(3P13) WILD-TYPE  89 108
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         73                         197 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         25                         108 
$`AMP PEAK  4(3P13) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       22.55        45.83         8.38        88.50        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       30.87         7.50        92.42        82.29        61.38        13.32 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      103.59         5.39        80.22        95.38        52.01         1.55 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA 
        9.90        13.22        35.80         9.99        44.52         4.93 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 
       17.56        14.83        13.15         0.00         0.00         0.20 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L 
        8.12         5.13        36.07         5.13         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GI 
       27.12         8.84         6.48         8.68        47.21        30.08 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MP TCGA-EE-A2MU 
       33.83         5.42         8.84        98.27        26.99         5.56 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 
       30.15        21.60        22.22        13.94        33.60        12.95 
TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV 
      114.15        28.60        36.07        12.62         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZK 
        1.71        85.74         6.71        23.80         7.30        12.89 
TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        3.22         2.27         7.23        31.33        84.72        10.13 
TCGA-GN-A268 
       15.42 

$`AMP PEAK  4(3P13) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB 
       28.08        81.24        10.29        85.32        21.14        68.22 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16         6.31        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       15.25        46.98        46.32        24.00         6.31         9.34 
TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       26.37        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       20.48        13.94        47.87         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        2.89        11.31        14.60        48.79        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       39.19        13.68        36.69        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X 
       19.36         7.00         0.20         0.13        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       10.55         6.31         1.12         1.35        12.20         4.31 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.34         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       11.15        38.63         8.55         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         2.43         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR 
       19.43        16.01        35.54        28.31        30.84         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       13.02        34.98        36.33         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.78       111.91        56.02        25.08        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16        23.05       124.31       122.73        25.84         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       16.14        27.35         0.46        31.40        18.61        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
       11.11        34.88         4.21        13.45        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        9.57        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 
       13.08        11.74         9.04        18.41         4.90         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.36        64.47         3.45        11.01        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.92        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A26A 
        0.43         9.90        12.85        24.85        16.24        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        10.65        11.05         5.79 

  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                       0.00                        0.13 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                     114.15                      124.31 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                      13.94                       14.20 
[1] "0.0 - 114.2 (13.9)" "0.1 - 124.3 (14.2)"
[1] "hr=" "1.7"
D4V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  4(3P13) MUTATED    49  25
  AMP PEAK  4(3P13) WILD-TYPE  93 109
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         74                         202 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         25                         109 
$`AMP PEAK  4(3P13) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       31.59        90.90        65.49       115.53        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       48.76       113.52       171.58       166.52        86.93        60.23 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      103.59        21.47       161.85       110.93       135.75       166.19 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA 
        9.90        66.25        36.03        35.93       107.34        65.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
      215.44        15.68        13.87        45.11        35.01         3.55 
TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H 
       12.20        94.98        68.15       109.64        78.87        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH 
        2.60        44.35        14.47       345.96       171.55       208.04 
TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MP 
       48.72        90.97        13.91        21.67       129.27       248.65 
TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
       53.26        54.51        36.95        53.19       101.79       148.08 
TCGA-ER-A197 TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A2NG TCGA-ER-A3ET 
       13.94       268.93        61.05        37.25        31.27        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FS-A1Z0 TCGA-FS-A1ZA 
       46.98        33.21       174.21       210.08       202.65        27.72 
TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
       23.93        50.14        77.88         7.23       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A268 
       10.13        62.79 

$`AMP PEAK  4(3P13) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB 
       28.08        95.74        43.43       103.10        23.77       168.00 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       58.06        46.98        46.32        24.53        13.87         9.34 
TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       39.75        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       51.68        15.06       137.92         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
       54.67         3.65         6.41        11.34         3.25        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        48.89       117.21        20.38       194.83       176.55 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        53.92        23.44        68.09        28.60        10.49 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y 
       10.16        17.85        52.01         6.35        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        33.73        14.70        26.89         4.96       151.27 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       39.62        72.07        18.61        56.42        37.35        55.92 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
       58.75        47.54        67.43       314.56       135.95        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        75.48       101.95        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      203.05       167.90        47.54        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       41.59       124.31       122.73        25.84         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       27.35        33.40        31.40        35.44        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        44.05       162.08        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       32.05       247.04        92.98         4.90        15.16         7.00 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45         0.20        22.92        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        9.90        14.04       120.46        64.44        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                       2.60                        0.16 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                     345.96                      357.37 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                     64.140                      45.715 
[1] "2.6 - 346.0 (64.1)" "0.2 - 357.4 (45.7)"
[1] "hr=" "2.1"
D4V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  4(3P13) MUTATED                   10             2
  AMP PEAK  4(3P13) WILD-TYPE                 27             2
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  4(3P13) MUTATED                                          15
  AMP PEAK  4(3P13) WILD-TYPE                                        45
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  4(3P13) MUTATED                    48
  AMP PEAK  4(3P13) WILD-TYPE                 131
D4V4, multiclass
                                           clus
vv                                          AMP PEAK  4(3P13) MUTATED
  DISTANT METASTASIS                                               10
  PRIMARY TUMOR                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        15
  REGIONAL LYMPH NODE                                              48
                                           clus
vv                                          AMP PEAK  4(3P13) WILD-TYPE
  DISTANT METASTASIS                                                 27
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          45
  REGIONAL LYMPH NODE                                               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  4(3P13) MUTATED             5       1       8        6        8
  AMP PEAK  4(3P13) WILD-TYPE           5       5      15        4       17
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  4(3P13) MUTATED          3         1         1         2         9
  AMP PEAK  4(3P13) WILD-TYPE       14         9        13         8        23
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  4(3P13) MUTATED            5          8          9        2
  AMP PEAK  4(3P13) WILD-TYPE          9         15         39       10
D4V5, multiclass
             clus
vv            AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  I OR II NOS                         5                           5
  STAGE 0                             1                           5
  STAGE I                             8                          15
  STAGE IA                            6                           4
  STAGE IB                            8                          17
  STAGE II                            3                          14
  STAGE IIA                           1                           9
  STAGE IIB                           1                          13
  STAGE IIC                           2                           8
  STAGE III                           9                          23
  STAGE IIIA                          5                           9
  STAGE IIIB                          8                          15
  STAGE IIIC                          9                          39
  STAGE IV                            2                          10
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  4(3P13) MUTATED      17 21 10 14
  AMP PEAK  4(3P13) WILD-TYPE    36 39 45 43
D4V6, multiclass
       clus
vv      AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  T0+T1                        17                          36
  T2                           21                          39
  T3                           10                          45
  T4                           14                          43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK  4(3P13) MUTATED    41  16   6   6
  AMP PEAK  4(3P13) WILD-TYPE 100  35  26  31
D4V7, multiclass
    clus
vv   AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  N0                        41                         100
  N1                        16                          35
  N2                         6                          26
  N3                         6                          31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  AMP PEAK  4(3P13) MUTATED    68   0   1   0   1
  AMP PEAK  4(3P13) WILD-TYPE 184   4   1   2   4
D4V8, multiclass
     clus
vv    AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  M0                         68                         184
  M1                          0                           4
  M1A                         1                           1
  M1B                         0                           2
  M1C                         1                           4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                             cls
clus                           0  1
  AMP PEAK  4(3P13) MUTATED   32 17
  AMP PEAK  4(3P13) WILD-TYPE 72 55
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     32   17
  AMP PEAK  4(3P13) WILD-TYPE   72   55
     clus
vv    AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  NO                         32                          72
  YES                        17                          55
[1] 2 2
[1] FALSE
D4V10, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED     7  69
  AMP PEAK  4(3P13) WILD-TYPE  27 178
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED      7   69
  AMP PEAK  4(3P13) WILD-TYPE   27  178
     clus
vv    AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  NO                          7                          27
  YES                        69                         178
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED    37  39
  AMP PEAK  4(3P13) WILD-TYPE  71 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     37   39
  AMP PEAK  4(3P13) WILD-TYPE   71  134
        clus
vv       AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  FEMALE                        37                          71
  MALE                          39                         134
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3P13) MUTATED       2                         0    74
  AMP PEAK  4(3P13) WILD-TYPE     3                         1   201
D4V13, multiclass
                           clus
vv                          AMP PEAK  4(3P13) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            74
                           clus
vv                          AMP PEAK  4(3P13) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             201
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED     0  76
  AMP PEAK  4(3P13) WILD-TYPE   3 198
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED      0   76
  AMP PEAK  4(3P13) WILD-TYPE    3  198
                        clus
vv                       AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                        76                         198
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(4Q12) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    25  27
  AMP PEAK  5(4Q12) WILD-TYPE 112 106
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         52                         218 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         27                         106 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51K 
        8.52        28.08        15.25        13.32        26.37        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
       23.11         2.89        11.31        48.79        35.80        39.19 
TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A181 TCGA-EE-A184 
       22.36        17.56         0.13         0.00         1.12         5.13 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GI 
        5.13        11.15         8.55        12.03        39.39        30.08 
TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AD 
        5.42        63.42        26.99        29.65       124.31         3.68 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B 
        3.22        21.60        22.22        33.60        12.95        25.18 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX 
        1.87         6.58        22.49         1.71        18.41         3.45 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 
       12.92        12.89        47.38         8.65         8.68        28.73 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
        7.23        31.33        15.42        14.70 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       16.47       111.09        32.42        70.16       110.79        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
      114.67        46.98        46.32        82.29        61.38        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       15.09        41.10         8.84        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6E9 
       52.01        47.87         1.55         6.97         4.01         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       13.22        14.60        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        36.69        25.15         4.93         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN 
        7.00        14.83        13.15         0.20         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
        0.20        11.57        10.55         6.31         8.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I 
       12.20         4.31        36.07         4.34         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        7.99         9.90        37.97        38.63         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       27.12         9.50         8.09         8.84         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67         8.94        34.29        17.98        34.92        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       111.78       111.91        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       21.60        27.16        23.05         5.56       122.73        25.84 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        13.81        15.95        12.72        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       16.14        27.35         0.46        13.94        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       38.40         5.72        76.41         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       11.80         1.51        13.08        12.62        11.74         9.04 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       85.74         4.90         6.71         3.58         5.36        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
       30.87        52.08         8.81        49.15        40.64        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
        0.82         5.23        53.85         3.22         7.36        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
        0.13         0.16         0.43         9.90        12.85        24.85 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        10.13        16.24        12.16        11.84        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                          0                           0 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     124.31                      122.73 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     14.975                      13.940 
[1] "0.0 - 124.3 (15.0)" "0.0 - 122.7 (13.9)"
[1] "hr=" "1.2"
D5V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    25  27
  AMP PEAK  5(4Q12) WILD-TYPE 117 107
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         52                         224 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         27                         107 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51K 
       16.67        28.08        58.06        60.23        39.75        18.38 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
      125.19         3.25        25.18        48.89        36.03       194.83 
TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A181 TCGA-EE-A184 
       23.44       215.44        17.85        35.01        33.73        68.15 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GI 
       78.87        13.97        72.07        56.42        47.54        48.72 
TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AD 
       13.91        96.23       248.65       103.56       124.31         3.68 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B 
      172.18        64.08        53.19       148.08        13.94        98.40 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX 
       23.34        80.32        46.98        33.21        92.98        48.59 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 
       47.38        23.93       101.26       133.55        26.56        28.73 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
        7.23       117.93        62.79        39.58 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       16.57       112.04       112.57        71.80       133.25        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
      130.72        46.98        46.32       166.52        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       40.14       131.90        10.03        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       166.19         7.43       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        3.65         6.41        11.34         9.90        66.25        22.95 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       53.92        65.92        68.09        28.60        10.49        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.16        45.11         3.55        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       12.20        29.82        27.22         8.65        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I 
       26.89         4.96       109.64       151.27       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       63.35        80.61        47.84        39.62        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       44.35        18.61        37.35        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        58.75        67.43       314.56       135.95       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       144.76       203.05       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       136.47        41.59        53.26       122.73        25.84 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81        23.47       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       34.32        27.35        33.40       101.79        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       50.76         9.17        77.75        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        20.15        16.37        31.27        32.05       247.04 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      174.21         4.90       210.08        15.16         7.00       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
       32.75        74.73        11.41       148.80        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
       27.09        27.02        77.82        50.14        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       47.54         0.16         2.40         9.90        14.04       120.46 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        10.13        64.44        32.48        46.36        12.62 
TCGA-OD-A75X TCGA-QB-A6FS 
      294.77         6.67 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       3.25                        0.16 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     248.65                      357.37 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     48.655                      47.540 
[1] "3.2 - 248.7 (48.7)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.1"
D5V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  5(4Q12) MUTATED                    6             1
  AMP PEAK  5(4Q12) WILD-TYPE                 31             3
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  5(4Q12) MUTATED                                          11
  AMP PEAK  5(4Q12) WILD-TYPE                                        49
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  5(4Q12) MUTATED                    33
  AMP PEAK  5(4Q12) WILD-TYPE                 146
D5V4, multiclass
                                           clus
vv                                          AMP PEAK  5(4Q12) MUTATED
  DISTANT METASTASIS                                                6
  PRIMARY TUMOR                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        11
  REGIONAL LYMPH NODE                                              33
                                           clus
vv                                          AMP PEAK  5(4Q12) WILD-TYPE
  DISTANT METASTASIS                                                 31
  PRIMARY TUMOR                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          49
  REGIONAL LYMPH NODE                                               146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  5(4Q12) MUTATED             1       0       7        1        7
  AMP PEAK  5(4Q12) WILD-TYPE           9       6      16        9       18
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  5(4Q12) MUTATED          2         0         1         4         8
  AMP PEAK  5(4Q12) WILD-TYPE       15        10        13         6        24
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  5(4Q12) MUTATED            3          7          6        2
  AMP PEAK  5(4Q12) WILD-TYPE         11         16         42       10
D5V5, multiclass
             clus
vv            AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  I OR II NOS                         1                           9
  STAGE 0                             0                           6
  STAGE I                             7                          16
  STAGE IA                            1                           9
  STAGE IB                            7                          18
  STAGE II                            2                          15
  STAGE IIA                           0                          10
  STAGE IIB                           1                          13
  STAGE IIC                           4                           6
  STAGE III                           8                          24
  STAGE IIIA                          3                          11
  STAGE IIIB                          7                          16
  STAGE IIIC                          6                          42
  STAGE IV                            2                          10
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  5(4Q12) MUTATED      13 15  6 13
  AMP PEAK  5(4Q12) WILD-TYPE    40 45 49 44
D5V6, multiclass
       clus
vv      AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  T0+T1                        13                          40
  T2                           15                          45
  T3                            6                          49
  T4                           13                          44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK  5(4Q12) MUTATED    28  11   6   5
  AMP PEAK  5(4Q12) WILD-TYPE 113  40  26  32
D5V7, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  N0                        28                         113
  N1                        11                          40
  N2                         6                          26
  N3                         5                          32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  AMP PEAK  5(4Q12) MUTATED    47   0   1   1   0
  AMP PEAK  5(4Q12) WILD-TYPE 205   4   1   1   5
D5V8, multiclass
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  M0                         47                         205
  M1                          0                           4
  M1A                         1                           1
  M1B                         1                           1
  M1C                         0                           5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                             cls
clus                           0  1
  AMP PEAK  5(4Q12) MUTATED   20 12
  AMP PEAK  5(4Q12) WILD-TYPE 84 60
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     20   12
  AMP PEAK  5(4Q12) WILD-TYPE   84   60
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                         20                          84
  YES                        12                          60
[1] 2 2
[1] FALSE
D5V10, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     7  45
  AMP PEAK  5(4Q12) WILD-TYPE  27 202
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      7   45
  AMP PEAK  5(4Q12) WILD-TYPE   27  202
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          7                          27
  YES                        45                         202
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    20  32
  AMP PEAK  5(4Q12) WILD-TYPE  88 141
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     20   32
  AMP PEAK  5(4Q12) WILD-TYPE   88  141
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        20                          88
  MALE                          32                         141
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED       1                         0    51
  AMP PEAK  5(4Q12) WILD-TYPE     4                         1   224
D5V13, multiclass
                           clus
vv                          AMP PEAK  5(4Q12) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            51
                           clus
vv                          AMP PEAK  5(4Q12) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     1  51
  AMP PEAK  5(4Q12) WILD-TYPE   2 223
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      1   51
  AMP PEAK  5(4Q12) WILD-TYPE    2  223
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                           2
  NOT HISPANIC OR LATINO                        51                         223
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(5P15.33) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(5P15.33) MUTATED   46 39
  AMP PEAK  6(5P15.33) WILD-TYPE 91 94
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            85                            185 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            39                             94 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JN 
        8.52        22.55        69.90        30.87         6.31        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MU 
       64.44        45.11        15.25        61.38        24.00        26.37 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       80.22        17.72         8.84        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        6.97        23.11         9.90        11.31        13.22        48.79 
TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       13.68         7.00        17.56        13.15         0.20         0.13 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I 
        8.12         1.12         5.13        36.07         9.21         1.18 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
       11.15        38.63         8.55        27.12         6.48         8.68 
TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS 
       11.31        28.31        98.27         2.70        26.99        27.16 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      124.31       122.73         3.68        30.15        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C 
        3.22        22.22        33.60        12.95        25.18         3.78 
TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND 
      114.15        28.60        42.84        34.68         9.57         1.87 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FS-A1YX 
       13.08        11.74         1.71        85.74         5.36         3.45 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F4 
       19.53         7.17        12.89         8.65         0.82         7.36 
TCGA-FS-A4F5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26D 
       28.73         0.13         7.23        31.33        84.72        14.70 
TCGA-GN-A4U9 
       10.65 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       88.50        68.22        11.41         7.50        36.16        92.42 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML 
      114.67        46.98        46.32        82.29        13.32         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34       103.59         5.39        42.71        15.09        41.10 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG 
       20.48        13.94        95.38         4.01         2.89        14.60 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        10.03        39.19         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       14.83         0.00         0.00        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
       10.55         6.31         1.35        12.20         4.31         4.34 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L 
        5.13         7.99         9.90        37.97         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       13.02        34.98        36.33         8.84         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.78       111.91        56.02        25.08        21.60        29.65 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 
       23.05         5.56        25.84        13.81        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       21.60        16.14        27.35         0.46        13.94        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E 
       18.61        38.40         5.72        76.41         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19W 
       11.11        34.88         4.21        13.45        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       78.44        11.80         1.51        12.62         9.04         6.58 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW 
       22.49        18.41         4.90         6.71         3.58        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        3.39        20.38         8.22        11.08        30.87        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        52.08         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.39         5.23        53.85         3.22        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.99         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 
        0.43         9.90        12.85        24.85        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       15.42        12.16        11.84        11.05         5.79 

  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                          0.13                           0.00 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                        124.31                         114.67 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                         13.22                          14.24 
[1] "0.1 - 124.3 (13.2)" "0.0 - 114.7 (14.2)"
[1] "hr=" "1.1"
D6V2, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(5P15.33) MUTATED   48 39
  AMP PEAK  6(5P15.33) WILD-TYPE 94 95
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            87                            189 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            39                             95 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JN 
       16.67        31.59        69.90        48.76        12.10        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MU 
       66.08        45.11        58.06        86.93        24.53        39.75 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
      161.85        18.38        10.03       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EA 
        7.43       125.19       151.53         3.65         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       66.25        48.89       176.55        10.49       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20B 
       10.16        17.85        94.98        33.73        68.15       109.64 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M 
      168.26        13.55        13.97        39.62        72.07        44.35 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 
      345.96       171.55        46.82        75.48       129.27        28.83 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      248.65       136.47       124.31       122.73         3.68        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 
       23.47       138.81       172.18        53.19       148.08        13.94 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       98.40        48.89       268.93        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FR-A44A 
       50.89        23.34        16.37        32.05        33.21       174.21 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZQ 
        7.00        48.59        40.27         9.70        23.93       133.55 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 
       27.09        66.67        28.73        47.54         7.23       117.93 
TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U9 
       84.72        39.58        12.62 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
      115.53       168.00        11.87       113.52        42.08       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML 
      130.72        46.98        46.32       166.52        60.23        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34       103.59        21.47        43.69        40.14       131.90 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 
       51.68        15.06       110.93        54.67         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.25        22.95        36.03       117.21        20.38       194.83 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       68.09        28.60        15.68        45.11        35.01         3.55 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A 
       14.70        26.89         4.96       151.27        78.87        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       80.61        47.84        32.19         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
       37.35        14.47        55.92        25.87        17.92       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       94.82        21.67        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54        43.23       103.56        41.59        53.26 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       25.84        13.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        33.40       101.79        31.40        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
        9.17        77.75        12.59        13.02        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        6.44       131.51        37.25       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       20.15        31.27       247.04        80.32        46.98        92.98 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.90       210.08        15.16       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       53.52        15.45        32.75        47.38       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        50.14       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        22.92         0.16         2.40         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       14.04       120.46        10.13        64.44        62.79        32.48 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       46.36       294.77         6.67 

  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                          3.65                           0.16 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                        345.96                         357.37 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                         48.89                          47.38 
[1] "3.6 - 346.0 (48.9)" "0.2 - 357.4 (47.4)"
[1] "hr=" "1.2"
D6V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  6(5P15.33) MUTATED                   11             4
  AMP PEAK  6(5P15.33) WILD-TYPE                 26             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  6(5P15.33) MUTATED                                          15
  AMP PEAK  6(5P15.33) WILD-TYPE                                        45
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  6(5P15.33) MUTATED                    58
  AMP PEAK  6(5P15.33) WILD-TYPE                 121
D6V4, multiclass
                                           clus
vv                                          AMP PEAK  6(5P15.33) MUTATED
  DISTANT METASTASIS                                                  11
  PRIMARY TUMOR                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           15
  REGIONAL LYMPH NODE                                                 58
                                           clus
vv                                          AMP PEAK  6(5P15.33) WILD-TYPE
  DISTANT METASTASIS                                                    26
  PRIMARY TUMOR                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             45
  REGIONAL LYMPH NODE                                                  121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  6(5P15.33) MUTATED             2       2       7        2        8
  AMP PEAK  6(5P15.33) WILD-TYPE           8       4      16        8       17
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  6(5P15.33) MUTATED          8         2         1         5
  AMP PEAK  6(5P15.33) WILD-TYPE        9         8        13         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  6(5P15.33) MUTATED           9          4          8         15
  AMP PEAK  6(5P15.33) WILD-TYPE        23         10         15         33
                                vv
clus                             STAGE IV
  AMP PEAK  6(5P15.33) MUTATED          4
  AMP PEAK  6(5P15.33) WILD-TYPE        8
D6V5, multiclass
             clus
vv            AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  I OR II NOS                            2                              8
  STAGE 0                                2                              4
  STAGE I                                7                             16
  STAGE IA                               2                              8
  STAGE IB                               8                             17
  STAGE II                               8                              9
  STAGE IIA                              2                              8
  STAGE IIB                              1                             13
  STAGE IIC                              5                              5
  STAGE III                              9                             23
  STAGE IIIA                             4                             10
  STAGE IIIB                             8                             15
  STAGE IIIC                            15                             33
  STAGE IV                               4                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK  6(5P15.33) MUTATED      21 15 16 18
  AMP PEAK  6(5P15.33) WILD-TYPE    32 45 39 39
D6V6, multiclass
       clus
vv      AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  T0+T1                           21                             32
  T2                              15                             45
  T3                              16                             39
  T4                              18                             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK  6(5P15.33) MUTATED   43 12 14 13
  AMP PEAK  6(5P15.33) WILD-TYPE 98 39 18 24
D6V7, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  N0                           43                             98
  N1                           12                             39
  N2                           14                             18
  N3                           13                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK  6(5P15.33) MUTATED    78   0   1   1   3
  AMP PEAK  6(5P15.33) WILD-TYPE 174   4   1   1   2
D6V8, multiclass
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  M0                            78                            174
  M1                             0                              4
  M1A                            1                              1
  M1B                            1                              1
  M1C                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                                cls
clus                              0  1
  AMP PEAK  6(5P15.33) MUTATED   32 21
  AMP PEAK  6(5P15.33) WILD-TYPE 72 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     32   21
  AMP PEAK  6(5P15.33) WILD-TYPE   72   51
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                            32                             72
  YES                           21                             51
[1] 2 2
[1] FALSE
D6V10, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    13  76
  AMP PEAK  6(5P15.33) WILD-TYPE  21 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     13   76
  AMP PEAK  6(5P15.33) WILD-TYPE   21  171
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                            13                             21
  YES                           76                            171
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    35  54
  AMP PEAK  6(5P15.33) WILD-TYPE  73 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     35   54
  AMP PEAK  6(5P15.33) WILD-TYPE   73  119
        clus
vv       AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  FEMALE                           35                             73
  MALE                             54                            119
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(5P15.33) MUTATED       3                         0    86
  AMP PEAK  6(5P15.33) WILD-TYPE     2                         1   189
D6V13, multiclass
                           clus
vv                          AMP PEAK  6(5P15.33) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               86
                           clus
vv                          AMP PEAK  6(5P15.33) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED     1  87
  AMP PEAK  6(5P15.33) WILD-TYPE   2 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      1   87
  AMP PEAK  6(5P15.33) WILD-TYPE    2  187
                        clus
vv                       AMP PEAK  6(5P15.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       AMP PEAK  6(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            187
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5Q35.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(5Q35.3) MUTATED    25  19
  AMP PEAK  7(5Q35.3) WILD-TYPE 112 114
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           44                           226 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           19                           114 
$`AMP PEAK  7(5Q35.3) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CF TCGA-D3-A3MU 
        8.52        30.87        56.19        45.11        24.00        26.37 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72         8.84         1.55        23.11         9.90        11.31 
TCGA-DA-A1IA TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29R 
        4.93         8.12         1.35         9.21         4.41         8.84 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
        6.48         8.68        19.43        27.16        23.05       124.31 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19P 
        3.22        22.22        33.60         3.78        11.11        34.68 
TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7U9 TCGA-FS-A1YX 
        1.87         9.04         6.58         1.71         5.36         3.45 
TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-FW-A3TU 
        8.22        12.92        12.89        28.73         0.20         0.13 
TCGA-GF-A6C8 TCGA-GN-A4U9 
       12.85        10.65 

$`AMP PEAK  7(5Q35.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
       36.16         6.31        92.42        64.44       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       46.98        46.32        82.29        61.38        13.32         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       41.10        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        6.97         4.01         2.89        13.22        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.00         0.00        13.22         0.20        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.34         5.13         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         8.55         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.09         9.99         2.43         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        47.21        30.08        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       21.60        29.65         5.56       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        13.81        15.95        12.72        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       21.60        16.14        27.35         0.46        13.94        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.90       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       28.60        42.84         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV 
       11.80         1.51        13.08        12.62        11.74        22.49 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW 
       18.41        85.74         4.90         6.71         3.58        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        3.39        20.38        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
        8.68        27.39         0.82         5.23        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        7.36        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 
        0.99         0.16         0.43         9.90         7.23        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        11.05         5.79 

  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                         0.13                          0.00 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                       124.31                        122.73 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                        9.555                        15.170 
[1] "0.1 - 124.3 (9.6)"  "0.0 - 122.7 (15.2)"
[1] "hr=" "1.2"
D7V2, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(5Q35.3) MUTATED    27  19
  AMP PEAK  7(5Q35.3) WILD-TYPE 115 115
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           46                           230 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           19                           115 
$`AMP PEAK  7(5Q35.3) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CF TCGA-D3-A3MU 
       16.67        48.76        56.19        45.11        24.53        39.75 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW 
       18.38        10.03       166.19       125.19       151.53         3.65 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20H 
        9.90        25.18        65.92        94.98        14.70       168.26 
TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GJ TCGA-EE-A2MS 
       32.19        14.47       345.96       171.55        89.33       136.47 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19C 
       41.59       124.31       172.18        53.19       148.08        48.89 
TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       26.37       162.08        23.34       247.04        80.32        33.21 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A4F5 
        7.00        48.59        53.52        47.38        23.93        28.73 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A4U9 
        0.20        47.54        14.04        12.62 

$`AMP PEAK  7(5Q35.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        66.08       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       46.98        46.32       166.52        86.93        60.23        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
      131.90        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GS TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
        7.43        54.67         6.41        11.34         3.25        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
      176.55        35.93       107.34        61.18        53.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.16        17.85        45.11        35.01         3.55        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        6.35        12.20        29.82        27.22         8.65        33.73 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       55.92        25.87        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        48.72        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       103.56 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       50.76         9.17        77.75        98.40        12.59        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       50.89        37.25       148.18        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       16.37        31.27        32.05        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.90       210.08        15.16       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZP 
       40.27        15.45         9.70        32.75       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
       27.09        27.02        77.82        50.14        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV 
       12.43        26.73        49.45        77.88        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        2.40         9.90         7.23       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       10.13        64.44        62.79        32.48        39.58        46.36 
TCGA-OD-A75X TCGA-QB-A6FS 
      294.77         6.67 

  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                         0.20                          0.16 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                       345.96                        357.37 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                        47.46                         48.28 
[1] "0.2 - 346.0 (47.5)" "0.2 - 357.4 (48.3)"
[1] "hr=" "1.2"
D7V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  7(5Q35.3) MUTATED                   10             2
  AMP PEAK  7(5Q35.3) WILD-TYPE                 27             2
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  7(5Q35.3) MUTATED                                           5
  AMP PEAK  7(5Q35.3) WILD-TYPE                                        55
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK  7(5Q35.3) MUTATED                    30
  AMP PEAK  7(5Q35.3) WILD-TYPE                 149
D7V4, multiclass
                                           clus
vv                                          AMP PEAK  7(5Q35.3) MUTATED
  DISTANT METASTASIS                                                 10
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           5
  REGIONAL LYMPH NODE                                                30
                                           clus
vv                                          AMP PEAK  7(5Q35.3) WILD-TYPE
  DISTANT METASTASIS                                                   27
  PRIMARY TUMOR                                                         2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            55
  REGIONAL LYMPH NODE                                                 149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  7(5Q35.3) MUTATED             1       1       5        3        5
  AMP PEAK  7(5Q35.3) WILD-TYPE           9       5      18        7       20
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  7(5Q35.3) MUTATED          2         1         1         1
  AMP PEAK  7(5Q35.3) WILD-TYPE       15         9        13         9
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  7(5Q35.3) MUTATED           4          3          2          8
  AMP PEAK  7(5Q35.3) WILD-TYPE        28         11         21         40
                               vv
clus                            STAGE IV
  AMP PEAK  7(5Q35.3) MUTATED          3
  AMP PEAK  7(5Q35.3) WILD-TYPE        9
D7V5, multiclass
             clus
vv            AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  I OR II NOS                           1                             9
  STAGE 0                               1                             5
  STAGE I                               5                            18
  STAGE IA                              3                             7
  STAGE IB                              5                            20
  STAGE II                              2                            15
  STAGE IIA                             1                             9
  STAGE IIB                             1                            13
  STAGE IIC                             1                             9
  STAGE III                             4                            28
  STAGE IIIA                            3                            11
  STAGE IIIB                            2                            21
  STAGE IIIC                            8                            40
  STAGE IV                              3                             9
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  7(5Q35.3) MUTATED      11 12  8  7
  AMP PEAK  7(5Q35.3) WILD-TYPE    42 48 47 50
D7V6, multiclass
       clus
vv      AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  T0+T1                          11                            42
  T2                             12                            48
  T3                              8                            47
  T4                              7                            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  7(5Q35.3) MUTATED    23   8   3   8
  AMP PEAK  7(5Q35.3) WILD-TYPE 118  43  29  29
D7V7, multiclass
    clus
vv   AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  N0                          23                           118
  N1                           8                            43
  N2                           3                            29
  N3                           8                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  AMP PEAK  7(5Q35.3) MUTATED    41   1   1   1   1
  AMP PEAK  7(5Q35.3) WILD-TYPE 211   3   1   1   4
D7V8, multiclass
     clus
vv    AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  M0                           41                           211
  M1                            1                             3
  M1A                           1                             1
  M1B                           1                             1
  M1C                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                               cls
clus                             0  1
  AMP PEAK  7(5Q35.3) MUTATED   20  9
  AMP PEAK  7(5Q35.3) WILD-TYPE 84 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED     20    9
  AMP PEAK  7(5Q35.3) WILD-TYPE   84   63
     clus
vv    AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  NO                           20                            84
  YES                           9                            63
[1] 2 2
[1] FALSE
D7V10, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED     5  42
  AMP PEAK  7(5Q35.3) WILD-TYPE  29 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED      5   42
  AMP PEAK  7(5Q35.3) WILD-TYPE   29  205
     clus
vv    AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  NO                            5                            29
  YES                          42                           205
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED    20  27
  AMP PEAK  7(5Q35.3) WILD-TYPE  88 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED     20   27
  AMP PEAK  7(5Q35.3) WILD-TYPE   88  146
        clus
vv       AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  FEMALE                          20                            88
  MALE                            27                           146
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5Q35.3) MUTATED       0                         0    47
  AMP PEAK  7(5Q35.3) WILD-TYPE     5                         1   228
D7V13, multiclass
                           clus
vv                          AMP PEAK  7(5Q35.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              47
                           clus
vv                          AMP PEAK  7(5Q35.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED     1  46
  AMP PEAK  7(5Q35.3) WILD-TYPE   2 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED      1   46
  AMP PEAK  7(5Q35.3) WILD-TYPE    2  228
                        clus
vv                       AMP PEAK  7(5Q35.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       AMP PEAK  7(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           228
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(6P24.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(6P24.3) MUTATED   66 86
  AMP PEAK  8(6P24.3) WILD-TYPE 71 47
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          152                           118 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                           86                            47 
$`AMP PEAK  8(6P24.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       16.47         8.52       110.79        22.55        45.83        81.24 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JO 
        8.38        21.14        68.22        30.87         7.50        64.44 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       15.25        61.38         6.31       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
       80.22        17.72        13.94        52.01        47.87        23.11 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        13.22        14.60        48.79        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44Q 
       13.68         9.99         4.93         6.64         7.00        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.13         0.00         0.00        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H 
        1.12        12.20         5.13         4.31        36.07         9.21 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P 
        7.99         9.90        11.15         8.55         1.08        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.84         9.99         2.43         8.09         9.67        39.39 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       17.98        47.21        19.43        35.54        33.83         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
        9.53        29.46        14.56        63.42       111.78        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       25.08        26.99        21.60        27.16         5.56       124.31 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        13.81        15.95         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       21.60        16.14        22.22        33.60        12.95         5.72 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M 
        3.78         3.52        11.90        11.11         4.21        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC 
       42.84        34.68         9.57        36.07        17.72        11.80 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P 
       13.08         9.04         6.58        22.49         1.71         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        6.71         3.58        64.47         3.45        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       15.52         7.30        20.38        19.53         7.17        30.87 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
       12.89        47.38        52.08         8.81        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         0.82         5.23         3.22        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 
       10.78         2.27         0.20         0.13         7.23        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       10.13        16.24        15.42        12.16        14.70        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

$`AMP PEAK  8(6P24.3) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 
      111.09        32.42        70.16        28.08        10.29        85.32 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       88.50        69.90        11.41        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        45.11       114.67        46.98        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       13.32        24.00         9.34        42.71        15.09        41.10 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 
        8.84        20.48        95.38         1.55         6.97         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 
        2.89        11.31        35.80        51.12        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R 
       25.15        22.36        19.36        17.56        14.83         0.20 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F 
       13.22         0.20        11.57         1.35         4.34         5.13 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
        1.18        37.97        38.63         4.41        27.12         9.50 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.09         6.48         8.68        11.31        49.22        23.90 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GM 
        8.94        34.29        34.92        30.08        16.01        28.31 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MH 
       30.84         8.84         6.18        47.51        44.25         7.96 
TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      111.91        29.65        23.05       122.73        25.84        30.15 
TCGA-EE-A3AH TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       12.72        27.35         0.46        13.94        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       38.40        76.41        25.18       114.15        34.88        13.45 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A3YN 
       78.44         1.87         1.51        12.62        11.74        18.41 
TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
       85.74         5.36        11.01         7.33         3.39         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A4F0 TCGA-FS-A4F4 
       11.08        12.92         8.65        49.15        53.85         7.36 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        5.98         6.41         0.99         0.16         0.43         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U8 
       12.85        24.85        84.72        11.84 

  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                         0.00                          0.16 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                       124.31                        122.73 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                       13.115                        18.510 
[1] "0.0 - 124.3 (13.1)" "0.2 - 122.7 (18.5)"
[1] "hr=" "1.8"
D8V2, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(6P24.3) MUTATED   70 86
  AMP PEAK  8(6P24.3) WILD-TYPE 72 48
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          156                           120 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                           86                            48 
$`AMP PEAK  8(6P24.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       16.57        16.67       133.25        31.59        90.90        95.74 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JO 
       65.49        23.77       168.00        48.76       113.52        66.08 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       58.06        86.93        13.87       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
      161.85        18.38        15.06       135.75       137.92       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
      151.53        54.67         3.65         9.90        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA 
       48.89        20.38       194.83       176.55        35.93        65.92 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       68.09        10.49        13.87        17.85        45.11        35.01 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
        3.55        27.22         8.65        94.98        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
       68.15         4.96       109.64       168.26        63.35        80.61 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       13.97        72.07         2.60        56.42        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH 
       25.87        17.92        39.29        47.54       314.56       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       89.33        79.66        90.97        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2ME 
       44.88        94.82       129.27        28.83        47.28       103.27 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66        96.23       144.76       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF 
       43.23       136.47        53.26       124.31         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       53.19       148.08        13.94         9.17        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       13.02        26.37         6.44        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES 
       50.89        37.25       148.18        43.82        16.37       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       80.32        46.98        33.21         4.90       210.08        15.16 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
      216.92        48.59       202.65        20.91        28.08        27.72 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
      357.37        40.27         9.70        32.75        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73        11.41        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
       27.02        50.14        28.73       174.84        12.43        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        0.20        47.54         7.23       117.93        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        32.48        39.58        12.62       294.77         6.67 

$`AMP PEAK  8(6P24.3) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 
      112.04       112.57        71.80        28.08        43.43       103.10 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
      115.53        69.90        11.87        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        45.11       130.72        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       60.23        24.53         9.34        43.69        40.14       131.90 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1JX 
       10.03        51.68       110.93       166.19         7.43         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I5 
       11.34         3.25        25.18        36.03       117.21       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       61.18        53.92        23.44        28.60       215.44        15.68 
TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 
       10.16        52.01         6.35        12.20        29.82        14.70 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
      151.27        78.87        13.55        47.84        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       44.35        18.61        37.35       345.96       171.55        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI 
      102.90        24.43        58.75        67.43       135.95        48.72 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       54.74        75.48       101.95        21.67        19.76        61.51 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB 
      103.20        16.96       203.05       103.56        41.59       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       25.84        54.51       138.81        27.35        33.40       101.79 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G 
       31.40        35.44        50.76        77.75        98.40       268.93 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
      152.35       131.51        79.99        23.34        20.15        31.27 
TCGA-ER-A2NH TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z7 
       32.05        92.98       174.21         7.00       228.59         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       48.85        53.52        15.45        47.38       133.55       148.80 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV 
       77.82        66.67        26.73        49.45        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U8 
        2.40         9.90        14.04       120.46        84.72        46.36 

  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                         0.20                          0.16 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                       357.37                        345.96 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                        47.54                         48.28 
[1] "0.2 - 357.4 (47.5)" "0.2 - 346.0 (48.3)"
[1] "hr=" "1.3"
D8V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  8(6P24.3) MUTATED                   26             3
  AMP PEAK  8(6P24.3) WILD-TYPE                 11             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  8(6P24.3) MUTATED                                          38
  AMP PEAK  8(6P24.3) WILD-TYPE                                        22
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK  8(6P24.3) MUTATED                    91
  AMP PEAK  8(6P24.3) WILD-TYPE                  88
D8V4, multiclass
                                           clus
vv                                          AMP PEAK  8(6P24.3) MUTATED
  DISTANT METASTASIS                                                 26
  PRIMARY TUMOR                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          38
  REGIONAL LYMPH NODE                                                91
                                           clus
vv                                          AMP PEAK  8(6P24.3) WILD-TYPE
  DISTANT METASTASIS                                                   11
  PRIMARY TUMOR                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            22
  REGIONAL LYMPH NODE                                                  88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  8(6P24.3) MUTATED             3       3      15        5       17
  AMP PEAK  8(6P24.3) WILD-TYPE           7       3       8        5        8
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  8(6P24.3) MUTATED         11         4         7         7
  AMP PEAK  8(6P24.3) WILD-TYPE        6         6         7         3
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  8(6P24.3) MUTATED          15         13         14         23
  AMP PEAK  8(6P24.3) WILD-TYPE        17          1          9         25
                               vv
clus                            STAGE IV
  AMP PEAK  8(6P24.3) MUTATED          6
  AMP PEAK  8(6P24.3) WILD-TYPE        6
D8V5, multiclass
             clus
vv            AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  I OR II NOS                           3                             7
  STAGE 0                               3                             3
  STAGE I                              15                             8
  STAGE IA                              5                             5
  STAGE IB                             17                             8
  STAGE II                             11                             6
  STAGE IIA                             4                             6
  STAGE IIB                             7                             7
  STAGE IIC                             7                             3
  STAGE III                            15                            17
  STAGE IIIA                           13                             1
  STAGE IIIB                           14                             9
  STAGE IIIC                           23                            25
  STAGE IV                              6                             6
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  8(6P24.3) MUTATED      26 35 31 39
  AMP PEAK  8(6P24.3) WILD-TYPE    27 25 24 18
D8V6, multiclass
       clus
vv      AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  T0+T1                          26                            27
  T2                             35                            25
  T3                             31                            24
  T4                             39                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  8(6P24.3) MUTATED   82 28 19 19
  AMP PEAK  8(6P24.3) WILD-TYPE 59 23 13 18
D8V7, multiclass
    clus
vv   AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  N0                          82                            59
  N1                          28                            23
  N2                          19                            13
  N3                          19                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  AMP PEAK  8(6P24.3) MUTATED   141   3   2   1   1
  AMP PEAK  8(6P24.3) WILD-TYPE 111   1   0   1   4
D8V8, multiclass
     clus
vv    AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  M0                          141                           111
  M1                            3                             1
  M1A                           2                             0
  M1B                           1                             1
  M1C                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                               cls
clus                             0  1
  AMP PEAK  8(6P24.3) MUTATED   60 44
  AMP PEAK  8(6P24.3) WILD-TYPE 44 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED     60   44
  AMP PEAK  8(6P24.3) WILD-TYPE   44   28
     clus
vv    AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  NO                           60                            44
  YES                          44                            28
[1] 2 2
[1] FALSE
D8V10, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P24.3) MUTATED    19 140
  AMP PEAK  8(6P24.3) WILD-TYPE  15 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED     19  140
  AMP PEAK  8(6P24.3) WILD-TYPE   15  107
     clus
vv    AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  NO                           19                            15
  YES                         140                           107
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, binary
                               cls
clus                             0  1
  AMP PEAK  8(6P24.3) MUTATED   63 96
  AMP PEAK  8(6P24.3) WILD-TYPE 45 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED     63   96
  AMP PEAK  8(6P24.3) WILD-TYPE   45   77
        clus
vv       AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  FEMALE                          63                            45
  MALE                            96                            77
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P24.3) MUTATED       3                         1   155
  AMP PEAK  8(6P24.3) WILD-TYPE     2                         0   120
D8V13, multiclass
                           clus
vv                          AMP PEAK  8(6P24.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             155
                           clus
vv                          AMP PEAK  8(6P24.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P24.3) MUTATED     2 155
  AMP PEAK  8(6P24.3) WILD-TYPE   1 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED      2  155
  AMP PEAK  8(6P24.3) WILD-TYPE    1  119
                        clus
vv                       AMP PEAK  8(6P24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         155
                        clus
vv                       AMP PEAK  8(6P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           119
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6Q12) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q12) MUTATED    30  30
  AMP PEAK  9(6Q12) WILD-TYPE 107 103
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         60                         210 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         30                         103 
$`AMP PEAK  9(6Q12) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JF TCGA-D3-A3CC 
        8.52       110.79         8.38        21.14        30.87        61.38 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EC 
       26.37        80.22        47.87        23.11         9.90        13.22 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 
       48.79        39.19        13.22         0.20        10.55         1.12 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A2GB TCGA-EE-A2GN TCGA-EE-A2GT 
       12.20         5.13        36.07        39.39        33.83        34.98 
TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       29.46        14.56        25.08        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      124.31         3.68         3.22        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N 
       22.22         5.72         3.78         3.52        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       34.68         9.57        36.07        11.80         1.51        13.08 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZW 
        6.58        22.49        23.80         7.30        47.38        27.39 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       14.20         0.13         7.23        10.13        16.24        15.42 

$`AMP PEAK  9(6Q12) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47       111.09        32.42        70.16        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB 
       45.83        81.24        10.29        85.32        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        11.41         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        45.11       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
      103.59         5.39        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
        8.84        20.48        13.94        95.38        52.01         1.55 
TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW 
        6.97         4.01         2.89        11.31        14.60        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       17.56        14.83        13.15         0.20         0.13         0.00 
TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A185 
        0.00        11.57         6.31         8.12         1.35         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        6.48         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
       30.84         5.42         1.15        13.02        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG 
       98.27         2.70         6.18        47.51         9.53        44.25 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
        7.96        63.42       111.78       111.91        56.02        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       21.60        29.65       122.73        25.84        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       15.95        12.72        22.92        27.35         0.46        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       33.60        31.40        18.61        12.95        38.40        76.41 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       25.18        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
       13.45        17.72        78.44         1.87        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        9.04         1.71        18.41        85.74         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
        3.58         5.36        64.47         3.45        11.01        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        12.89        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
        8.65         8.81        49.15        40.64         8.68         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
        5.23        53.85         3.22         7.36        28.73        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.99         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.43         9.90        12.85        24.85        31.33        84.72 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        14.70        11.84        10.65        11.05         5.79 

  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                       0.13                        0.00 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                     124.31                      122.73 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                     18.690                      13.385 
[1] "0.1 - 124.3 (18.7)" "0.0 - 122.7 (13.4)"
[1] "hr=" "1"  
D9V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q12) MUTATED    32  30
  AMP PEAK  9(6Q12) WILD-TYPE 110 104
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         62                         214 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         30                         104 
$`AMP PEAK  9(6Q12) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JF TCGA-D3-A3CC 
       16.67       133.25        65.49        23.77        48.76        86.93 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW 
       39.75       161.85       137.92       125.19        54.67         3.65 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EB-A5UN TCGA-EB-A6L9 
        9.90        66.25        48.89       194.83        52.01        12.20 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A2GB 
       27.22        33.73        26.89        68.15       109.64        47.54 
TCGA-EE-A2GN TCGA-EE-A2GT TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MN TCGA-EE-A2MS 
       90.97        44.88       103.27       204.66        47.54       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J5 
       41.59        53.26       124.31         3.68       172.18        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       64.08        34.32        53.19         9.17        48.89        12.59 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC 
       61.05        44.05       162.08        50.89        37.25        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1Z0 TCGA-FS-A1ZA 
       20.15        16.37        80.32        46.98       202.65        27.72 
TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A266 
      101.26        49.48       174.84        47.54         7.23        10.13 
TCGA-GN-A267 TCGA-GN-A268 
       64.44        62.79 

$`AMP PEAK  9(6Q12) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57       112.04       112.57        71.80        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB 
       90.90        95.74        43.43       103.10       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        45.11       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
      103.59        21.47        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       10.03        51.68        15.06       110.93       135.75       166.19 
TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
        7.43       151.53         6.41        11.34         3.25        25.18 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95        36.03       117.21        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EE-A17X 
       17.85        45.11        35.01         3.55         6.35        29.82 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        8.65        94.98        14.70         4.96       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        37.35        14.47        55.92       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       58.75        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
       89.33        54.74        79.66        75.48       101.95        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ 
       19.76        61.51        47.28       103.20        16.96        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      144.76       203.05       167.90       248.65        43.23       103.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84        54.51        13.81        23.47       138.81 
TCGA-EE-A3J4 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      127.20        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E 
       35.44        13.94        50.76        77.75        98.40        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19W 
       26.37       268.93       152.35         6.44       131.51       148.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL 
       79.99        23.34        31.27        32.05       247.04        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21         4.90       210.08        15.16         7.00 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        22.92         0.16         2.40         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D 
       14.04       120.46       117.93        84.72        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                       3.65                        0.16 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                     204.66                      357.37 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                     49.185                      46.900 
[1] "3.6 - 204.7 (49.2)" "0.2 - 357.4 (46.9)"
[1] "hr=" "1"  
D9V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  9(6Q12) MUTATED                   10             3
  AMP PEAK  9(6Q12) WILD-TYPE                 27             1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  9(6Q12) MUTATED                                          17
  AMP PEAK  9(6Q12) WILD-TYPE                                        43
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  9(6Q12) MUTATED                    33
  AMP PEAK  9(6Q12) WILD-TYPE                 146
D9V4, multiclass
                                           clus
vv                                          AMP PEAK  9(6Q12) MUTATED
  DISTANT METASTASIS                                               10
  PRIMARY TUMOR                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        17
  REGIONAL LYMPH NODE                                              33
                                           clus
vv                                          AMP PEAK  9(6Q12) WILD-TYPE
  DISTANT METASTASIS                                                 27
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          43
  REGIONAL LYMPH NODE                                               146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK  9(6Q12) MUTATED             1       3       5        3       10
  AMP PEAK  9(6Q12) WILD-TYPE           9       3      18        7       15
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  9(6Q12) MUTATED          4         2         2         3         5
  AMP PEAK  9(6Q12) WILD-TYPE       13         8        12         7        27
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  9(6Q12) MUTATED            6          5          5        0
  AMP PEAK  9(6Q12) WILD-TYPE          8         18         43       12
D9V5, multiclass
             clus
vv            AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  I OR II NOS                         1                           9
  STAGE 0                             3                           3
  STAGE I                             5                          18
  STAGE IA                            3                           7
  STAGE IB                           10                          15
  STAGE II                            4                          13
  STAGE IIA                           2                           8
  STAGE IIB                           2                          12
  STAGE IIC                           3                           7
  STAGE III                           5                          27
  STAGE IIIA                          6                           8
  STAGE IIIB                          5                          18
  STAGE IIIC                          5                          43
  STAGE IV                            0                          12
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK  9(6Q12) MUTATED      11 17  9 14
  AMP PEAK  9(6Q12) WILD-TYPE    42 43 46 43
D9V6, multiclass
       clus
vv      AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  T0+T1                        11                          42
  T2                           17                          43
  T3                            9                          46
  T4                           14                          43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK  9(6Q12) MUTATED    34  12   5   5
  AMP PEAK  9(6Q12) WILD-TYPE 107  39  27  32
D9V7, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  N0                        34                         107
  N1                        12                          39
  N2                         5                          27
  N3                         5                          32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  AMP PEAK  9(6Q12) MUTATED    58   0   0   0   0
  AMP PEAK  9(6Q12) WILD-TYPE 194   4   2   2   5
D9V8, multiclass
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  M0                         58                         194
  M1                          0                           4
  M1A                         0                           2
  M1B                         0                           2
  M1C                         0                           5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                             cls
clus                           0  1
  AMP PEAK  9(6Q12) MUTATED   27 13
  AMP PEAK  9(6Q12) WILD-TYPE 77 59
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     27   13
  AMP PEAK  9(6Q12) WILD-TYPE   77   59
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                         27                          77
  YES                        13                          59
[1] 2 2
[1] FALSE
D9V10, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED     8  55
  AMP PEAK  9(6Q12) WILD-TYPE  26 192
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED      8   55
  AMP PEAK  9(6Q12) WILD-TYPE   26  192
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                          8                          26
  YES                        55                         192
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED    20  43
  AMP PEAK  9(6Q12) WILD-TYPE  88 130
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     20   43
  AMP PEAK  9(6Q12) WILD-TYPE   88  130
        clus
vv       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  FEMALE                        20                          88
  MALE                          43                         130
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6Q12) MUTATED       2                         0    61
  AMP PEAK  9(6Q12) WILD-TYPE     3                         1   214
D9V13, multiclass
                           clus
vv                          AMP PEAK  9(6Q12) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            61
                           clus
vv                          AMP PEAK  9(6Q12) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED     0  62
  AMP PEAK  9(6Q12) WILD-TYPE   3 212
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED      0   62
  AMP PEAK  9(6Q12) WILD-TYPE    3  212
                        clus
vv                       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                        62                         212
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7P22.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(7P22.1) MUTATED   75 74
  AMP PEAK 10(7P22.1) WILD-TYPE 62 59
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          149                           121 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                           74                            59 
$`AMP PEAK 10(7P22.1) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
       16.47         8.52       111.09        32.42        70.16        22.55 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       21.14        88.50        69.90        11.41        92.42        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        46.98        46.32        82.29        61.38 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51N 
        6.31         9.34       103.59        26.37        41.10         8.84 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       20.48        52.01         1.55         6.97        23.11         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        11.31        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       25.15         4.93         6.64        17.56        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        0.13        13.22         0.20        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
        1.12        36.07         9.21         7.99        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       38.63         1.08         9.50        12.03         8.09         6.48 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
        8.68        11.31         8.94        39.39        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       30.08        19.43        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK 
        5.42         8.84        98.27         2.70        63.42       111.78 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31       122.73         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A199 
       15.95        12.72         3.22        22.92        21.60         5.72 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       25.18         3.78        11.90       114.15        34.88         4.21 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL 
       28.60        34.68        36.07         1.87        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74         4.90         6.71         3.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       64.47        14.24        15.52         7.33        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       19.53        30.87        12.89        47.38         8.65         8.81 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 
        0.82         5.23         3.22        28.73        14.20         0.20 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.43         7.23        31.33        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       12.16        14.70        11.84        10.65         5.79 

$`AMP PEAK 10(7P22.1) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        28.08        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
        8.38        68.22        30.87         7.50        36.16         6.31 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E 
       64.44        15.25        13.32        24.00         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       42.71        15.09        17.72        13.94        95.38        47.87 
TCGA-D9-A3Z1 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        4.01        39.19        22.36        19.36         7.00        14.83 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        0.00         0.00        11.57         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G 
        4.31         4.34         5.13         1.18         9.90         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        4.41        27.12         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GK 
       49.22        23.90         9.67        34.29        17.98        16.01 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC 
        1.15        13.02        34.98        36.33         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML 
        9.53        29.46        44.25         7.96        14.56       111.91 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       23.05        25.84        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N 
       38.40        76.41         3.52        11.11        13.45        42.84 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        9.57        17.72        78.44        11.80         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FS-A1YX TCGA-FS-A1YY 
       12.62        11.74         9.04         6.58         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       23.80         7.30         3.39        11.08         7.17        12.92 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 
       52.08        49.15        40.64         8.68        27.39        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
        7.36        10.78         5.98         6.41         2.27         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
        0.13         0.16         9.90        12.85        24.85        84.72 
TCGA-OD-A75X 
       11.05 

  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                         0.13                          0.00 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       124.31                        111.91 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                        15.42                         13.08 
[1] "0.1 - 124.3 (15.4)" "0.0 - 111.9 (13.1)"
[1] "hr=" "1.1"
D10V2, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(7P22.1) MUTATED   78 75
  AMP PEAK 10(7P22.1) WILD-TYPE 64 59
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          153                           123 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                           75                            59 
$`AMP PEAK 10(7P22.1) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
       16.57        16.67       112.04       112.57        71.80        31.59 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       23.77       115.53        69.90        11.87       171.58        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        46.98        46.32       166.52        86.93 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51N 
       13.87         9.34       103.59        39.75       131.90        10.03 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       51.68       135.75       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       54.67         6.41         3.25         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       22.95        48.89        36.03       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       35.93       107.34        61.18        53.92        65.92        68.09 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
      215.44        13.87        10.16        17.85         3.55        52.01 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B 
       12.20        27.22         8.65        94.98        33.73       109.64 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
      168.26        63.35        47.84        13.97        39.62         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       18.61        56.42        37.35       345.96       171.55        46.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       58.75        47.54       135.95       208.04        48.72        89.33 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 
       79.66        75.48        90.97       101.95        13.91        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
      129.27        28.83        96.23       144.76       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       103.56       136.47        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
      172.18       127.20        64.08         9.17        98.40        48.89 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P 
       13.02       268.93       152.35         6.44        61.05       162.08 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       37.25        23.34        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1Z3 
        4.90       210.08        15.16         7.00       216.92        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZH 
       28.08         7.79       357.37        53.52        40.27        32.75 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       23.93       101.26       133.55        11.41        27.09        27.02 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO 
       50.14        28.73       174.84         0.20         2.40         7.23 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        10.13        64.44        62.79        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       46.36        12.62         6.67 

$`AMP PEAK 10(7P22.1) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       65.49       168.00        48.76       113.52        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E 
       66.08        58.06        60.23        24.53        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       43.69        40.14        18.38        15.06       110.93       137.92 
TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
        3.65        11.34       194.83        23.44        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A182 
       15.68        45.11        35.01         6.35        29.82        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       151.27        78.87        13.55 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S 
       80.61        72.07        32.19        44.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
       25.87        17.92       102.90        24.43        39.29        67.43 
TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      314.56        54.74        14.30        55.59        44.88        94.82 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J5 TCGA-EE-A3J8 
      204.66       203.05        41.59        25.84        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F 
       35.44        13.94        50.76        77.75        12.59        26.37 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      131.51        44.05        50.89       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZF 
       48.59       228.59       202.65        27.72        48.85        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
        9.70        47.38        74.73       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       49.48        77.82        66.67        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 
       77.88        22.92        47.54         0.16         9.90        14.04 
TCGA-GN-A262 TCGA-GN-A265 TCGA-OD-A75X 
      120.46        84.72       294.77 

  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                         0.20                          0.16 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       357.37                        314.56 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                        48.89                         45.11 
[1] "0.2 - 357.4 (48.9)" "0.2 - 314.6 (45.1)"
[1] "hr=" "1.1"
D10V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 10(7P22.1) MUTATED                   18             3
  AMP PEAK 10(7P22.1) WILD-TYPE                 19             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 10(7P22.1) MUTATED                                          35
  AMP PEAK 10(7P22.1) WILD-TYPE                                        25
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK 10(7P22.1) MUTATED                    99
  AMP PEAK 10(7P22.1) WILD-TYPE                  80
D10V4, multiclass
                                           clus
vv                                          AMP PEAK 10(7P22.1) MUTATED
  DISTANT METASTASIS                                                 18
  PRIMARY TUMOR                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          35
  REGIONAL LYMPH NODE                                                99
                                           clus
vv                                          AMP PEAK 10(7P22.1) WILD-TYPE
  DISTANT METASTASIS                                                   19
  PRIMARY TUMOR                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            25
  REGIONAL LYMPH NODE                                                  80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 10(7P22.1) MUTATED             7       1      15        5        8
  AMP PEAK 10(7P22.1) WILD-TYPE           3       5       8        5       17
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 10(7P22.1) MUTATED         10         5         6         8
  AMP PEAK 10(7P22.1) WILD-TYPE        7         5         8         2
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 10(7P22.1) MUTATED          20         10         13         25
  AMP PEAK 10(7P22.1) WILD-TYPE        12          4         10         23
                               vv
clus                            STAGE IV
  AMP PEAK 10(7P22.1) MUTATED          9
  AMP PEAK 10(7P22.1) WILD-TYPE        3
D10V5, multiclass
             clus
vv            AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  I OR II NOS                           7                             3
  STAGE 0                               1                             5
  STAGE I                              15                             8
  STAGE IA                              5                             5
  STAGE IB                              8                            17
  STAGE II                             10                             7
  STAGE IIA                             5                             5
  STAGE IIB                             6                             8
  STAGE IIC                             8                             2
  STAGE III                            20                            12
  STAGE IIIA                           10                             4
  STAGE IIIB                           13                            10
  STAGE IIIC                           25                            23
  STAGE IV                              9                             3
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 10(7P22.1) MUTATED      35 28 32 31
  AMP PEAK 10(7P22.1) WILD-TYPE    18 32 23 26
D10V6, multiclass
       clus
vv      AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  T0+T1                          35                            18
  T2                             28                            32
  T3                             32                            23
  T4                             31                            26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 10(7P22.1) MUTATED   75 32 16 23
  AMP PEAK 10(7P22.1) WILD-TYPE 66 19 16 14
D10V7, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  N0                          75                            66
  N1                          32                            19
  N2                          16                            16
  N3                          23                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  AMP PEAK 10(7P22.1) MUTATED   137   3   2   1   4
  AMP PEAK 10(7P22.1) WILD-TYPE 115   1   0   1   1
D10V8, multiclass
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  M0                          137                           115
  M1                            3                             1
  M1A                           2                             0
  M1B                           1                             1
  M1C                           4                             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                               cls
clus                             0  1
  AMP PEAK 10(7P22.1) MUTATED   57 38
  AMP PEAK 10(7P22.1) WILD-TYPE 47 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     57   38
  AMP PEAK 10(7P22.1) WILD-TYPE   47   34
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                           57                            47
  YES                          38                            34
[1] 2 2
[1] FALSE
D10V10, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED    23 132
  AMP PEAK 10(7P22.1) WILD-TYPE  11 115
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     23  132
  AMP PEAK 10(7P22.1) WILD-TYPE   11  115
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                           23                            11
  YES                         132                           115
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, binary
                               cls
clus                             0  1
  AMP PEAK 10(7P22.1) MUTATED   59 96
  AMP PEAK 10(7P22.1) WILD-TYPE 49 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     59   96
  AMP PEAK 10(7P22.1) WILD-TYPE   49   77
        clus
vv       AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  FEMALE                          59                            49
  MALE                            96                            77
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7P22.1) MUTATED       5                         0   150
  AMP PEAK 10(7P22.1) WILD-TYPE     0                         1   125
D10V13, multiclass
                           clus
vv                          AMP PEAK 10(7P22.1) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             150
                           clus
vv                          AMP PEAK 10(7P22.1) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED     2 151
  AMP PEAK 10(7P22.1) WILD-TYPE   1 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED      2  151
  AMP PEAK 10(7P22.1) WILD-TYPE    1  123
                        clus
vv                       AMP PEAK 10(7P22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         151
                        clus
vv                       AMP PEAK 10(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           123
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7Q34) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 11(7Q34) MUTATED   80 80
  AMP PEAK 11(7Q34) WILD-TYPE 57 53
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        160                         110 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                         80                          53 
$`AMP PEAK 11(7Q34) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.47         8.52        32.42        70.16        22.55        45.83 
TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       85.32        21.14        88.50        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       36.16        92.42        56.19        45.11        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        61.38        13.32         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N 
      103.59        26.37         5.39        80.22        41.10         8.84 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       20.48        52.01         1.55         6.97        23.11         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        11.31        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       25.15         4.93         6.64        17.56        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
        0.13        13.22         0.20        10.55         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        1.35        12.20        36.07         9.21         7.99        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
        6.48         8.68        11.31         8.94        39.39        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
       47.21        30.08        35.54        28.31        30.84         5.42 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MJ 
       34.98        98.27         2.70         6.18         7.96        63.42 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
      111.78        56.02        21.60        29.65        27.16         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      124.31       122.73        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JH 
        3.22        22.92        21.60        21.60        27.35        13.94 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       31.40        12.95        38.40         5.72        25.18         3.78 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P 
       11.90       114.15        34.88         4.21        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3PL 
        9.57        36.07         1.87        13.08         6.58         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YX 
       18.41        85.74         4.90         6.71         5.36         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
       23.80         7.33        20.38         8.22        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ 
       30.87        47.38         8.65         8.81        49.15         5.23 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY 
        3.22         7.36        28.73        14.20         0.20         0.43 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        7.23        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-QB-A6FS 
       12.16        14.70        10.65         5.79 

$`AMP PEAK 11(7Q34) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      111.09       110.79        28.08        81.24        10.29         8.38 
TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CF 
       68.22        30.87         6.31        64.44       114.67        24.00 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       42.71        15.09        17.72        13.94        95.38        47.87 
TCGA-D9-A3Z1 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44R 
        4.01        39.19        22.36        19.36         7.00         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A184 TCGA-EE-A185 
        0.00         0.00        11.57         6.31         5.13         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
        4.34         5.13         1.18         9.90        11.15         8.55 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        8.09         8.84         9.99         2.43         8.09        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK 
       23.90         9.67        34.29        17.98        19.43        16.01 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC 
       33.83         1.15        13.02        36.33         8.84        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN 
        9.53        29.46        44.25        14.56       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JA 
       26.99        23.05        25.84         3.68        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F 
        0.46        33.60        18.61        76.41         3.52        11.11 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       13.45        42.84        17.72        78.44        11.80         1.51 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YW 
       12.62        11.74         9.04        22.49         3.58        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE 
       11.01        14.24        15.52         7.30         3.39        19.53 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       12.92        12.89        52.08        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        0.82        53.85        10.78         5.98         6.41         2.27 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
        0.99         0.13         0.16         9.90        12.85        24.85 
TCGA-GN-A4U8 TCGA-OD-A75X 
       11.84        11.05 

  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                       0.13                        0.00 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                     124.31                      114.67 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                     14.765                      12.970 
[1] "0.1 - 124.3 (14.8)" "0.0 - 114.7 (13.0)"
[1] "hr=" "1.1"
D11V2, survival
                             sevent
clus2                          0  1
  AMP PEAK 11(7Q34) MUTATED   84 81
  AMP PEAK 11(7Q34) WILD-TYPE 58 53
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        165                         111 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                         81                          53 
$`AMP PEAK 11(7Q34) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.57        16.67       112.57        71.80        31.59        90.90 
TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
      103.10        23.77       115.53        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       42.08       171.58        56.19        45.11        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        60.23        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N 
      103.59        39.75        21.47       161.85       131.90        10.03 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       51.68       135.75       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       54.67         3.65         6.41         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       66.25        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL 
       68.09       215.44        15.68        13.87        17.85         3.55 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       52.01        12.20        27.22        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       26.89       109.64       168.26        63.35        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T 
       32.19         2.60        44.35        18.61        56.42       345.96 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      171.55        46.82        58.75        47.54       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT 
       48.72        79.66        75.48       101.95        13.91        44.88 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
      129.27        28.83        19.76        16.96        96.23       144.76 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      167.90        43.23       103.56       136.47        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 
      127.20        36.95        64.08        27.35       101.79        31.40 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
       13.94        50.76         9.17        98.40        48.89        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      268.93       152.35         6.44        61.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       37.25        23.34        16.37        80.32        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z0 
      174.21         4.90       210.08         7.00        48.59       202.65 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.79       357.37        53.52        15.45         9.70        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F2 
      101.26       133.55        11.41       148.80        27.02        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO 
       66.67        28.73       174.84         0.20         2.40         7.23 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-QB-A6FS 
       39.58        12.62         6.67 

$`AMP PEAK 11(7Q34) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      112.04       133.25        28.08        95.74        43.43        65.49 
TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CF 
      168.00        48.76        12.10        66.08       130.72        24.53 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       43.69        40.14        18.38        15.06       110.93       137.92 
TCGA-D9-A3Z1 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44R 
       11.34       194.83        23.44        28.60        10.49        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A184 
       45.11        35.01         6.35        29.82         8.65        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D 
        4.96       151.27        78.87        13.55        80.61        13.97 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       72.07        37.35        14.47        55.92        25.87        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ 
      102.90        24.43        39.29        67.43       314.56        89.33 
TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
       54.74        90.97        14.30        55.59        94.82        21.67 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML 
       61.51        47.28       103.27       103.20       204.66       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 
       47.54       248.65        41.59        25.84         3.68        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D 
       53.19        33.40       148.08        35.44        77.75        12.59 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       26.37       131.51        44.05       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A7U8 
       20.15        31.27        32.05       247.04        46.98        15.16 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      216.92       228.59        20.91        28.08        27.72        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU 
       40.27        47.38        23.93        74.73        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       49.48        27.09        77.82        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 
       77.88        22.92        47.54         0.16         9.90        14.04 
TCGA-GN-A262 TCGA-GN-A4U8 TCGA-OD-A75X 
      120.46        46.36       294.77 

  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                       0.20                        0.16 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                     357.37                      314.56 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                      50.76                       45.11 
[1] "0.2 - 357.4 (50.8)" "0.2 - 314.6 (45.1)"
[1] "hr=" "1"  
D11V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 11(7Q34) MUTATED                   15             4
  AMP PEAK 11(7Q34) WILD-TYPE                 22             0
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 11(7Q34) MUTATED                                          41
  AMP PEAK 11(7Q34) WILD-TYPE                                        19
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK 11(7Q34) MUTATED                   108
  AMP PEAK 11(7Q34) WILD-TYPE                  71
D11V4, multiclass
                                           clus
vv                                          AMP PEAK 11(7Q34) MUTATED
  DISTANT METASTASIS                                               15
  PRIMARY TUMOR                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        41
  REGIONAL LYMPH NODE                                             108
                                           clus
vv                                          AMP PEAK 11(7Q34) WILD-TYPE
  DISTANT METASTASIS                                                 22
  PRIMARY TUMOR                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          19
  REGIONAL LYMPH NODE                                                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 11(7Q34) MUTATED            10       2      12        6       12
  AMP PEAK 11(7Q34) WILD-TYPE           0       4      11        4       13
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 11(7Q34) MUTATED         10         6         3         8        23
  AMP PEAK 11(7Q34) WILD-TYPE        7         4        11         2         9
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 11(7Q34) MUTATED           12         15         26        8
  AMP PEAK 11(7Q34) WILD-TYPE          2          8         22        4
D11V5, multiclass
             clus
vv            AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  I OR II NOS                        10                           0
  STAGE 0                             2                           4
  STAGE I                            12                          11
  STAGE IA                            6                           4
  STAGE IB                           12                          13
  STAGE II                           10                           7
  STAGE IIA                           6                           4
  STAGE IIB                           3                          11
  STAGE IIC                           8                           2
  STAGE III                          23                           9
  STAGE IIIA                         12                           2
  STAGE IIIB                         15                           8
  STAGE IIIC                         26                          22
  STAGE IV                            8                           4
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK 11(7Q34) MUTATED      36 33 35 33
  AMP PEAK 11(7Q34) WILD-TYPE    17 27 20 24
D11V6, multiclass
       clus
vv      AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  T0+T1                        36                          17
  T2                           33                          27
  T3                           35                          20
  T4                           33                          24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  AMP PEAK 11(7Q34) MUTATED   79 37 20 23
  AMP PEAK 11(7Q34) WILD-TYPE 62 14 12 14
D11V7, multiclass
    clus
vv   AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  N0                        79                          62
  N1                        37                          14
  N2                        20                          12
  N3                        23                          14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  AMP PEAK 11(7Q34) MUTATED   152   2   2   1   4
  AMP PEAK 11(7Q34) WILD-TYPE 100   2   0   1   1
D11V8, multiclass
     clus
vv    AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  M0                        152                         100
  M1                          2                           2
  M1A                         2                           0
  M1B                         1                           1
  M1C                         4                           1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                             cls
clus                           0  1
  AMP PEAK 11(7Q34) MUTATED   66 41
  AMP PEAK 11(7Q34) WILD-TYPE 38 31
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     66   41
  AMP PEAK 11(7Q34) WILD-TYPE   38   31
     clus
vv    AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  NO                         66                          38
  YES                        41                          31
[1] 2 2
[1] FALSE
D11V10, binary
                             cls
clus                            0   1
  AMP PEAK 11(7Q34) MUTATED    23 146
  AMP PEAK 11(7Q34) WILD-TYPE  11 101
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     23  146
  AMP PEAK 11(7Q34) WILD-TYPE   11  101
     clus
vv    AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  NO                         23                          11
  YES                       146                         101
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, binary
                             cls
clus                           0  1
  AMP PEAK 11(7Q34) MUTATED   72 97
  AMP PEAK 11(7Q34) WILD-TYPE 36 76
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     72   97
  AMP PEAK 11(7Q34) WILD-TYPE   36   76
        clus
vv       AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  FEMALE                        72                          36
  MALE                          97                          76
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q34) MUTATED       4                         0   165
  AMP PEAK 11(7Q34) WILD-TYPE     1                         1   110
D11V13, multiclass
                           clus
vv                          AMP PEAK 11(7Q34) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                           165
                           clus
vv                          AMP PEAK 11(7Q34) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                             cls
clus                            0   1
  AMP PEAK 11(7Q34) MUTATED     1 165
  AMP PEAK 11(7Q34) WILD-TYPE   2 109
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED      1  165
  AMP PEAK 11(7Q34) WILD-TYPE    2  109
                        clus
vv                       AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             1                           2
  NOT HISPANIC OR LATINO                       165                         109
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8Q11.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(8Q11.21) MUTATED   65 60
  AMP PEAK 12(8Q11.21) WILD-TYPE 72 73
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                           125                            145 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                            60                             73 
$`AMP PEAK 12(8Q11.21) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA 
       16.47        70.16        81.24        10.29        85.32        88.50 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       69.90        30.87        56.19        64.44        45.11        15.25 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       82.29        61.38        13.32       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       80.22        41.10        17.72        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
       23.11        11.31        13.22        14.60        35.80        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       39.19        13.68         9.99        17.56        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
        0.13         0.00         0.00         0.20        10.55         6.31 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
        1.12        36.07        37.97        38.63         8.55         8.84 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        6.48         2.43         9.67        17.98        34.92        47.21 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
       35.54        28.31        33.83        30.84         5.42        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA 
        2.70         6.18         7.96        25.08        29.65       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73         3.68        30.15        15.95         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G 
       21.60        21.60        22.22        12.95         3.78       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S 
       34.88         4.21        13.45        28.60        42.84        36.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       11.80         1.87        13.08         6.58        22.49        85.74 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        6.71         3.58         5.36         3.45        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.33        20.38         8.22        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
        8.65         8.81        49.15        40.64         8.68         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD 
        3.22         7.36        28.73        14.20         5.98         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.20         0.16         9.90        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-OD-A75X TCGA-QB-A6FS 
       16.24        12.16        14.70        11.05         5.79 

$`AMP PEAK 12(8Q11.21) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
        8.52       111.09        32.42       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       45.83         8.38        21.14        68.22        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       36.16         6.31        92.42       114.67        46.98        46.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N 
       24.00         6.31         9.34        42.71        15.09         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       20.48        13.94        95.38        47.87         4.01         2.89 
TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        9.90        48.79        10.03        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        4.93        22.36         6.64        19.36         7.00        14.83 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       13.22        11.57         8.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        9.90        11.15         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.09         9.99         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI 
       49.22        23.90         8.94        39.39        34.29        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       19.43        16.01         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
        8.84        47.51         9.53        29.46        44.25        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
       63.42       111.78       111.91        56.02        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH 
       27.16        23.05         5.56        25.84        13.81        12.72 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       18.61        38.40         5.72        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       11.90        11.11        34.68         9.57        17.72        78.44 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
        1.51        12.62        11.74         9.04         1.71        18.41 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        4.90        64.47        11.01        14.24         7.30         3.39 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW 
       19.53        11.08         7.17        30.87        12.92        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.23        53.85        10.78         6.41         0.99         0.13 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A4U8 
        0.43         7.23        12.85        24.85        15.42        11.84 
TCGA-GN-A4U9 
       10.65 

  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                          0.00                           0.13 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                        124.31                         114.67 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                         15.25                          13.22 
[1] "0.0 - 124.3 (15.2)" "0.1 - 114.7 (13.2)"
[1] "hr=" "1.1"
D12V2, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(8Q11.21) MUTATED   65 60
  AMP PEAK 12(8Q11.21) WILD-TYPE 77 74
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                           125                            151 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                            60                             74 
$`AMP PEAK 12(8Q11.21) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA 
       16.57        71.80        95.74        43.43       103.10       115.53 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       69.90        48.76        56.19        66.08        45.11        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
      166.52        86.93        60.23       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
      161.85       131.90        18.38       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
      125.19        25.18        66.25        22.95        36.03       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
      194.83       176.55        35.93       215.44        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
       17.85        45.11        35.01        12.20        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
       33.73       109.64        47.84        39.62        72.07        14.47 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
      345.96        25.87        39.29       314.56       135.95       208.04 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
       79.66        75.48        90.97       101.95        13.91       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA 
       28.83        19.76        16.96        47.54       103.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73         3.68        54.51        23.47       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G 
       36.95        64.08        53.19        13.94        48.89       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S 
      152.35         6.44       131.51        61.05        44.05        37.25 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       43.82        23.34        16.37        80.32        46.98       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 
      210.08        15.16         7.00        48.59       202.65        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.79       357.37        53.52        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
      133.55        11.41       148.80        53.16        26.56        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD 
       50.14        66.67        28.73       174.84        26.73        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.20         0.16         9.90       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-OD-A75X TCGA-QB-A6FS 
       64.44        32.48        39.58       294.77         6.67 

$`AMP PEAK 12(8Q11.21) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.04       112.57       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       90.90        65.49        23.77       168.00        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       42.08        12.10       171.58       130.72        46.98        46.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N 
       24.53        13.87         9.34        43.69        40.14        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A149 
       51.68        15.06       110.93       137.92       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV 
        3.65         6.41        11.34         3.25         9.90        48.89 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EB-A5UN 
       68.09        28.60        10.49        15.68         3.55        52.01 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.35        29.82        94.98        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       80.61        13.97        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       56.42        37.35        55.92       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI 
      102.90        24.43        58.75        47.54        67.43        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       89.33        54.74        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
       21.67        61.51        47.28       103.27       103.20       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       144.76       203.05       167.90       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH 
      136.47        41.59        53.26        25.84        13.81       138.81 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       35.44        50.76         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       13.02        26.37       162.08        50.89       148.18        79.99 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
       20.15        31.27        32.05       247.04        33.21        92.98 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        4.90       216.92       228.59        20.91        27.72        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW 
       40.27        15.45         9.70        32.75        47.38        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
       27.02        77.82        12.43        49.45        22.92        47.54 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A4U8 
        2.40         7.23        14.04       120.46        62.79        46.36 
TCGA-GN-A4U9 
       12.62 

  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                          0.16                           2.40 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                        357.37                         248.65 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                         53.16                          46.82 
[1] "0.2 - 357.4 (53.2)" "2.4 - 248.7 (46.8)"
[1] "hr=" "1.3"
D12V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 12(8Q11.21) MUTATED                   15             3
  AMP PEAK 12(8Q11.21) WILD-TYPE                 22             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 12(8Q11.21) MUTATED                                          36
  AMP PEAK 12(8Q11.21) WILD-TYPE                                        24
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 12(8Q11.21) MUTATED                    72
  AMP PEAK 12(8Q11.21) WILD-TYPE                 107
D12V4, multiclass
                                           clus
vv                                          AMP PEAK 12(8Q11.21) MUTATED
  DISTANT METASTASIS                                                  15
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           36
  REGIONAL LYMPH NODE                                                 72
                                           clus
vv                                          AMP PEAK 12(8Q11.21) WILD-TYPE
  DISTANT METASTASIS                                                    22
  PRIMARY TUMOR                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             24
  REGIONAL LYMPH NODE                                                  107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 12(8Q11.21) MUTATED             5       1      12        3        9
  AMP PEAK 12(8Q11.21) WILD-TYPE           5       5      11        7       16
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 12(8Q11.21) MUTATED         10         4         4         5
  AMP PEAK 12(8Q11.21) WILD-TYPE        7         6        10         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 12(8Q11.21) MUTATED          22          8          8         22
  AMP PEAK 12(8Q11.21) WILD-TYPE        10          6         15         26
                                vv
clus                             STAGE IV
  AMP PEAK 12(8Q11.21) MUTATED          3
  AMP PEAK 12(8Q11.21) WILD-TYPE        9
D12V5, multiclass
             clus
vv            AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  I OR II NOS                            5                              5
  STAGE 0                                1                              5
  STAGE I                               12                             11
  STAGE IA                               3                              7
  STAGE IB                               9                             16
  STAGE II                              10                              7
  STAGE IIA                              4                              6
  STAGE IIB                              4                             10
  STAGE IIC                              5                              5
  STAGE III                             22                             10
  STAGE IIIA                             8                              6
  STAGE IIIB                             8                             15
  STAGE IIIC                            22                             26
  STAGE IV                               3                              9
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 12(8Q11.21) MUTATED      30 29 23 23
  AMP PEAK 12(8Q11.21) WILD-TYPE    23 31 32 34
D12V6, multiclass
       clus
vv      AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  T0+T1                           30                             23
  T2                              29                             31
  T3                              23                             32
  T4                              23                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 12(8Q11.21) MUTATED   58 29 13 17
  AMP PEAK 12(8Q11.21) WILD-TYPE 83 22 19 20
D12V7, multiclass
    clus
vv   AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  N0                           58                             83
  N1                           29                             22
  N2                           13                             19
  N3                           17                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 12(8Q11.21) MUTATED   116   2   0   0   1
  AMP PEAK 12(8Q11.21) WILD-TYPE 136   2   2   2   4
D12V8, multiclass
     clus
vv    AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  M0                           116                            136
  M1                             2                              2
  M1A                            0                              2
  M1B                            0                              2
  M1C                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q11.21) MUTATED   41 31
  AMP PEAK 12(8Q11.21) WILD-TYPE 63 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q11.21) MUTATED     41   31
  AMP PEAK 12(8Q11.21) WILD-TYPE   63   41
     clus
vv    AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  NO                            41                             63
  YES                           31                             41
[1] 2 2
[1] FALSE
D12V10, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q11.21) MUTATED    20 107
  AMP PEAK 12(8Q11.21) WILD-TYPE  14 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q11.21) MUTATED     20  107
  AMP PEAK 12(8Q11.21) WILD-TYPE   14  140
     clus
vv    AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  NO                            20                             14
  YES                          107                            140
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q11.21) MUTATED   46 81
  AMP PEAK 12(8Q11.21) WILD-TYPE 62 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q11.21) MUTATED     46   81
  AMP PEAK 12(8Q11.21) WILD-TYPE   62   92
        clus
vv       AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  FEMALE                           46                             62
  MALE                             81                             92
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q11.21) MUTATED       5                         0   122
  AMP PEAK 12(8Q11.21) WILD-TYPE     0                         1   153
D12V13, multiclass
                           clus
vv                          AMP PEAK 12(8Q11.21) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              122
                           clus
vv                          AMP PEAK 12(8Q11.21) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q11.21) MUTATED     1 124
  AMP PEAK 12(8Q11.21) WILD-TYPE   2 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q11.21) MUTATED      1  124
  AMP PEAK 12(8Q11.21) WILD-TYPE    2  150
                        clus
vv                       AMP PEAK 12(8Q11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          124
                        clus
vv                       AMP PEAK 12(8Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            150
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8Q24.21) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(8Q24.21) MUTATED   71 71
  AMP PEAK 13(8Q24.21) WILD-TYPE 66 62
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           142                            128 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                            71                             62 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.47       111.09        70.16        22.55        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO 
       85.32        88.50        69.90        30.87        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       45.11        15.25        82.29        61.38        13.32         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J 
        9.34       103.59        26.37         5.39        80.22        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       17.72         8.84        52.01         1.55         6.97        23.11 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        14.60        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       39.19        13.68         9.99         7.00        17.56        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y 
        0.20         0.13         0.00         0.00         0.20        10.55 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        6.31         1.12        36.07        37.97        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        4.41         1.08         8.84         9.99         6.48         2.43 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM 
        9.67        17.98        34.92        47.21        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       33.83        30.84         5.42        13.02        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
        6.18         7.96        63.42        25.08        26.99        29.65 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 
      124.31       122.73         3.68        30.15        15.95         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A198 
       22.92        21.60        21.60        22.22        12.95        38.40 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        3.78       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       42.84         9.57        36.07        11.80         1.87        13.08 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
        9.04         6.58        22.49        85.74         6.71         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        5.36        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.33        20.38         8.22        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
        8.65         8.81        49.15        40.64         8.68         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD 
        3.22         7.36        28.73        14.20         5.98         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        0.20         0.16         9.90        10.13        16.24        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        11.05         5.79 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
        8.52        32.42       110.79        28.08        45.83         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       21.14        68.22        11.41         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A51F 
       92.42       114.67        46.98        46.32        24.00        42.71 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A3Z1 
       15.09        20.48        13.94        95.38        47.87         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        2.89         9.90        48.79        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5UN 
        4.93        22.36         6.64        19.36        14.83        13.22 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       11.57         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29W 
       11.15        27.12         9.50        12.03         8.09         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        23.90         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GT 
       34.29        30.08        19.43        16.01         1.15        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       36.33         8.84        47.51         9.53        29.46        44.25 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS 
       14.56       111.78       111.91        56.02        21.60        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 
       23.05         5.56        25.84        13.81        12.72        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        5.72        76.41        25.18         3.52        11.90        11.11 
TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
       34.68        17.72        78.44         1.51        12.62        11.74 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        1.71        18.41         4.90        14.24         7.30         3.39 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW 
       19.53        11.08         7.17        30.87        12.92        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.23        53.85        10.78         6.41         0.99         0.13 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.43         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A268 TCGA-GN-A4U9 
       15.42        10.65 

  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          0.00                           0.13 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        124.31                         114.67 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        13.565                         14.400 
[1] "0.0 - 124.3 (13.6)" "0.1 - 114.7 (14.4)"
[1] "hr=" "1"  
D13V2, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(8Q24.21) MUTATED   72 71
  AMP PEAK 13(8Q24.21) WILD-TYPE 70 63
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           143                            133 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                            71                             63 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.57       112.04        71.80        31.59        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO 
      103.10       115.53        69.90        48.76        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       45.11        58.06       166.52        86.93        60.23        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J 
        9.34       103.59        39.75        21.47       161.85       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       18.38        10.03       135.75       166.19         7.43       125.19 
TCGA-D9-A1JW TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
        3.65        25.18        66.25        22.95        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 
       20.38       194.83       176.55        35.93        10.49       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 
       13.87        10.16        17.85        45.11        35.01        12.20 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E 
       27.22         8.65        33.73       109.64        47.84        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       72.07        32.19         2.60        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL 
       25.87        39.29       314.56       135.95       208.04        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       75.48        90.97       101.95        13.91        55.59       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP 
       28.83        19.76        16.96        96.23        47.54       248.65 
TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
      103.56       124.31       122.73         3.68        54.51        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 
      172.18       127.20        36.95        64.08        53.19        13.94 
TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       50.76        48.89       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND 
       61.05        44.05        50.89        37.25        43.82        23.34 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 
       16.37       247.04        80.32        46.98       174.21       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       15.16         7.00       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM 
       28.08         7.79       357.37        53.52        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       27.09        50.14        66.67        28.73       174.84        26.73 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 
       77.88         0.20         0.16         9.90        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        39.58        46.36       294.77         6.67 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
       16.67       112.57       133.25        28.08        90.90        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       168.00        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A51F 
      171.58       130.72        46.98        46.32        24.53        43.69 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A148 
       40.14        51.68        15.06       110.93       137.92       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV 
       54.67         6.41        11.34         3.25         9.90        48.89 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       28.60        15.68         3.55        52.01         6.35        29.82 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       94.98        14.70        26.89        68.15         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       78.87       168.26        13.55        63.35        80.61        13.97 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A29X 
       44.35        18.61        56.42        37.35       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        24.43        58.75        47.54        67.43 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU 
       48.72        89.33        54.74        14.30        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
       21.67        61.51        47.28       103.27       103.20       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      144.76       203.05       167.90        43.23       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JD 
       53.26        25.84        13.81       138.81        34.32        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 
       33.40       101.79       148.08        31.40        35.44         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P 
       77.75        98.40        12.59        13.02        26.37       162.08 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3PL 
      148.18        79.99        20.15        31.27        32.05        33.21 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE 
       92.98         4.90        20.91        27.72        48.85        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       15.45         9.70        32.75        47.38        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY 
       77.82        12.43        49.45        22.92        47.54         2.40 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        7.23        14.04       120.46       117.93        84.72        62.79 
TCGA-GN-A4U9 
       12.62 

  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          0.16                           2.40 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        357.37                         204.66 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                         50.14                          46.98 
[1] "0.2 - 357.4 (50.1)" "2.4 - 204.7 (47.0)"
[1] "hr=" "1.2"
D13V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 13(8Q24.21) MUTATED                   17             3
  AMP PEAK 13(8Q24.21) WILD-TYPE                 20             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 13(8Q24.21) MUTATED                                          39
  AMP PEAK 13(8Q24.21) WILD-TYPE                                        21
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 13(8Q24.21) MUTATED                    86
  AMP PEAK 13(8Q24.21) WILD-TYPE                  93
D13V4, multiclass
                                           clus
vv                                          AMP PEAK 13(8Q24.21) MUTATED
  DISTANT METASTASIS                                                  17
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           39
  REGIONAL LYMPH NODE                                                 86
                                           clus
vv                                          AMP PEAK 13(8Q24.21) WILD-TYPE
  DISTANT METASTASIS                                                    20
  PRIMARY TUMOR                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             21
  REGIONAL LYMPH NODE                                                   93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 13(8Q24.21) MUTATED             5       1      13        4       11
  AMP PEAK 13(8Q24.21) WILD-TYPE           5       5      10        6       14
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 13(8Q24.21) MUTATED         10         6         4         5
  AMP PEAK 13(8Q24.21) WILD-TYPE        7         4        10         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 13(8Q24.21) MUTATED          24          9         11         24
  AMP PEAK 13(8Q24.21) WILD-TYPE         8          5         12         24
                                vv
clus                             STAGE IV
  AMP PEAK 13(8Q24.21) MUTATED          5
  AMP PEAK 13(8Q24.21) WILD-TYPE        7
D13V5, multiclass
             clus
vv            AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  I OR II NOS                            5                              5
  STAGE 0                                1                              5
  STAGE I                               13                             10
  STAGE IA                               4                              6
  STAGE IB                              11                             14
  STAGE II                              10                              7
  STAGE IIA                              6                              4
  STAGE IIB                              4                             10
  STAGE IIC                              5                              5
  STAGE III                             24                              8
  STAGE IIIA                             9                              5
  STAGE IIIB                            11                             12
  STAGE IIIC                            24                             24
  STAGE IV                               5                              7
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 13(8Q24.21) MUTATED      35 32 27 27
  AMP PEAK 13(8Q24.21) WILD-TYPE    18 28 28 30
D13V6, multiclass
       clus
vv      AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  T0+T1                           35                             18
  T2                              32                             28
  T3                              27                             28
  T4                              27                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 13(8Q24.21) MUTATED   66 31 18 20
  AMP PEAK 13(8Q24.21) WILD-TYPE 75 20 14 17
D13V7, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  N0                           66                             75
  N1                           31                             20
  N2                           18                             14
  N3                           20                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 13(8Q24.21) MUTATED   133   2   1   0   2
  AMP PEAK 13(8Q24.21) WILD-TYPE 119   2   1   2   3
D13V8, multiclass
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  M0                           133                            119
  M1                             2                              2
  M1A                            1                              1
  M1B                            0                              2
  M1C                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                                cls
clus                              0  1
  AMP PEAK 13(8Q24.21) MUTATED   49 36
  AMP PEAK 13(8Q24.21) WILD-TYPE 55 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     49   36
  AMP PEAK 13(8Q24.21) WILD-TYPE   55   36
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                            49                             55
  YES                           36                             36
[1] 2 2
[1] FALSE
D13V10, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED    21 125
  AMP PEAK 13(8Q24.21) WILD-TYPE  13 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     21  125
  AMP PEAK 13(8Q24.21) WILD-TYPE   13  122
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                            21                             13
  YES                          125                            122
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, binary
                                cls
clus                              0  1
  AMP PEAK 13(8Q24.21) MUTATED   53 93
  AMP PEAK 13(8Q24.21) WILD-TYPE 55 80
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     53   93
  AMP PEAK 13(8Q24.21) WILD-TYPE   55   80
        clus
vv       AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  FEMALE                           53                             55
  MALE                             93                             80
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8Q24.21) MUTATED       5                         0   141
  AMP PEAK 13(8Q24.21) WILD-TYPE     0                         1   134
D13V13, multiclass
                           clus
vv                          AMP PEAK 13(8Q24.21) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              141
                           clus
vv                          AMP PEAK 13(8Q24.21) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED     1 143
  AMP PEAK 13(8Q24.21) WILD-TYPE   2 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      1  143
  AMP PEAK 13(8Q24.21) WILD-TYPE    2  131
                        clus
vv                       AMP PEAK 13(8Q24.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          143
                        clus
vv                       AMP PEAK 13(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            131
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(11Q13.3) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(11Q13.3) MUTATED    25  26
  AMP PEAK 14(11Q13.3) WILD-TYPE 112 107
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            51                            219 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            26                            107 
$`AMP PEAK 14(11Q13.3) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP 
       22.55        10.29        68.22        69.90        30.87        45.11 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D9-A3Z3 TCGA-D9-A6EC 
       82.29        13.32        24.00        80.22         2.89        13.22 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A20F 
        7.00        13.15         0.00         0.20         8.12         5.13 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GR 
        8.68         8.09        39.39        47.21         5.42         1.15 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MM TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19M 
        8.84        47.51        56.02        22.22        33.60        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       42.84         9.57        17.72        13.08         9.04         6.58 
TCGA-FR-A729 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZK 
        6.71        64.47         3.45         3.39         8.22        12.89 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO 
        8.65        49.15        40.64         3.22         2.27         7.23 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
       10.13        15.42        14.70 

$`AMP PEAK 14(11Q13.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        45.83        81.24        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       88.50        11.41         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        64.44       114.67        15.25        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       61.38         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       13.94        95.38        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       23.11         4.01         9.90        11.31        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       19.36        17.56        14.83         0.20         0.13         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       13.22        11.57        10.55         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H 
       12.20         5.13         4.31        36.07         4.34         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
        8.09         8.84         9.99         6.48         2.43        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        23.90         9.67         8.94        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       33.83        30.84        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       14.56        63.42       111.78       111.91        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35         0.46        13.94        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       34.68        36.07        78.44        11.80         1.87         1.51 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       12.62        11.74        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90         3.58         5.36        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
       15.52         7.33         7.30        20.38        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
        7.17        30.87        12.92        47.38        52.08         8.81 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       28.73        14.20        10.78         5.98         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
        0.99         0.13         0.16         0.43         9.90        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 
       24.85        31.33        84.72        16.24        12.16        11.84 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       10.65        11.05         5.79 

  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                             0                              0 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                         82.29                         124.31 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                         13.08                          14.60 
[1] "0.0 - 82.3 (13.1)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.1"
D14V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(11Q13.3) MUTATED    25  26
  AMP PEAK 14(11Q13.3) WILD-TYPE 117 108
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            51                            225 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            26                            108 
$`AMP PEAK 14(11Q13.3) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP 
       31.59        43.43       168.00        69.90        48.76        45.11 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D9-A3Z3 TCGA-D9-A6EC 
      166.52        60.23        24.53       161.85         3.25        66.25 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A20F 
       10.49        13.87        35.01        12.20        94.98        78.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GR 
      171.55        17.92        47.54       208.04        13.91        14.30 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MM TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19M 
       21.67        61.51       167.90        53.19       148.08        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       44.05        50.89       148.18        16.37       247.04        80.32 
TCGA-FR-A729 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZK 
      210.08       216.92        48.59        48.85        53.52        23.93 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO 
      133.55       148.80        53.16        50.14        77.88         7.23 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
       10.13        62.79        39.58 

$`AMP PEAK 14(11Q13.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        90.90        95.74       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
      115.53        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        66.08       130.72        58.06        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       86.93        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       15.06       110.93       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       53.92        65.92        23.44        68.09        28.60       215.44 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       15.68        10.16        17.85        45.11         3.55        52.01 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        6.35        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H 
       26.89        68.15         4.96       109.64       151.27       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
       37.35        14.47        55.92       345.96        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        24.43        39.29        58.75        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      135.95        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       90.97       101.95        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       28.83        19.76        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66        96.23       144.76       203.05        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
      162.08        37.25        79.99        43.82        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       31.27        32.05        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90        15.16         7.00       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
       28.08         7.79        27.72       357.37        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
        9.70        32.75        47.38       101.26        74.73        11.41 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       28.73       174.84        12.43        26.73        49.45         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       22.92        47.54         0.16         2.40         9.90        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 
      120.46       117.93        84.72        64.44        32.48        46.36 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                          3.25                           0.16 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                        247.04                         357.37 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                         53.16                          46.98 
[1] "3.2 - 247.0 (53.2)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.1"
D14V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 14(11Q13.3) MUTATED                    8             2
  AMP PEAK 14(11Q13.3) WILD-TYPE                 29             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 14(11Q13.3) MUTATED                                           8
  AMP PEAK 14(11Q13.3) WILD-TYPE                                        52
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 14(11Q13.3) MUTATED                    36
  AMP PEAK 14(11Q13.3) WILD-TYPE                 143
D14V4, multiclass
                                           clus
vv                                          AMP PEAK 14(11Q13.3) MUTATED
  DISTANT METASTASIS                                                   8
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            8
  REGIONAL LYMPH NODE                                                 36
                                           clus
vv                                          AMP PEAK 14(11Q13.3) WILD-TYPE
  DISTANT METASTASIS                                                    29
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             52
  REGIONAL LYMPH NODE                                                  143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 14(11Q13.3) MUTATED             6       2       8        1        4
  AMP PEAK 14(11Q13.3) WILD-TYPE           4       4      15        9       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 14(11Q13.3) MUTATED          4         1         2         2
  AMP PEAK 14(11Q13.3) WILD-TYPE       13         9        12         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 14(11Q13.3) MUTATED           5          2          5          6
  AMP PEAK 14(11Q13.3) WILD-TYPE        27         12         18         42
                                vv
clus                             STAGE IV
  AMP PEAK 14(11Q13.3) MUTATED          0
  AMP PEAK 14(11Q13.3) WILD-TYPE       12
D14V5, multiclass
             clus
vv            AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  I OR II NOS                            6                              4
  STAGE 0                                2                              4
  STAGE I                                8                             15
  STAGE IA                               1                              9
  STAGE IB                               4                             21
  STAGE II                               4                             13
  STAGE IIA                              1                              9
  STAGE IIB                              2                             12
  STAGE IIC                              2                              8
  STAGE III                              5                             27
  STAGE IIIA                             2                             12
  STAGE IIIB                             5                             18
  STAGE IIIC                             6                             42
  STAGE IV                               0                             12
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 14(11Q13.3) MUTATED       8 17  5 11
  AMP PEAK 14(11Q13.3) WILD-TYPE    45 43 50 46
D14V6, multiclass
       clus
vv      AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  T0+T1                            8                             45
  T2                              17                             43
  T3                               5                             50
  T4                              11                             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 14(11Q13.3) MUTATED    33   7   3   6
  AMP PEAK 14(11Q13.3) WILD-TYPE 108  44  29  31
D14V7, multiclass
    clus
vv   AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  N0                           33                            108
  N1                            7                             44
  N2                            3                             29
  N3                            6                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 14(11Q13.3) MUTATED    48   0   0   0   0
  AMP PEAK 14(11Q13.3) WILD-TYPE 204   4   2   2   5
D14V8, multiclass
     clus
vv    AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  M0                            48                            204
  M1                             0                              4
  M1A                            0                              2
  M1B                            0                              2
  M1C                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                                cls
clus                              0  1
  AMP PEAK 14(11Q13.3) MUTATED   17 12
  AMP PEAK 14(11Q13.3) WILD-TYPE 87 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED     17   12
  AMP PEAK 14(11Q13.3) WILD-TYPE   87   60
     clus
vv    AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  NO                            17                             87
  YES                           12                             60
[1] 2 2
[1] FALSE
D14V10, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q13.3) MUTATED     7  47
  AMP PEAK 14(11Q13.3) WILD-TYPE  27 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      7   47
  AMP PEAK 14(11Q13.3) WILD-TYPE   27  200
     clus
vv    AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  NO                             7                             27
  YES                           47                            200
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q13.3) MUTATED    22  32
  AMP PEAK 14(11Q13.3) WILD-TYPE  86 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED     22   32
  AMP PEAK 14(11Q13.3) WILD-TYPE   86  141
        clus
vv       AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  FEMALE                           22                             86
  MALE                             32                            141
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(11Q13.3) MUTATED       2                         1    51
  AMP PEAK 14(11Q13.3) WILD-TYPE     3                         0   224
D14V13, multiclass
                           clus
vv                          AMP PEAK 14(11Q13.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               51
                           clus
vv                          AMP PEAK 14(11Q13.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q13.3) MUTATED     0  54
  AMP PEAK 14(11Q13.3) WILD-TYPE   3 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      0   54
  AMP PEAK 14(11Q13.3) WILD-TYPE    3  220
                        clus
vv                       AMP PEAK 14(11Q13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       AMP PEAK 14(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            220
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(11Q13.4) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(11Q13.4) MUTATED    24  23
  AMP PEAK 15(11Q13.4) WILD-TYPE 113 110
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                            47                            223 
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                            23                            110 
$`AMP PEAK 15(11Q13.4) MUTATED`
TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE 
       10.29        69.90        30.87        45.11        82.29        13.32 
TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 
       24.00         2.89        13.22        13.15         0.00         0.20 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GP 
        8.68         8.09        39.39        34.29        47.21         5.42 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MM TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19L 
        8.84        47.51        56.02        22.22        33.60        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       28.60        42.84         9.57        13.08         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZB 
       22.49         1.71         6.71        64.47         3.45         3.39 
TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4F2 
        8.22        12.89         8.65        49.15        40.64         3.22 
TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
        2.27         7.23        10.13        15.42        14.70 

$`AMP PEAK 15(11Q13.4) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        45.83        81.24        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        88.50        68.22        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
        6.31        92.42        56.19        64.44       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98        46.32        61.38         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       17.72         8.84        20.48        13.94        95.38        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 
       47.87         1.55         6.97        23.11         4.01         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        14.60        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X 
       14.83         0.20         0.13         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
        8.09         8.84         9.99         6.48         2.43        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE 
       49.22        23.90         9.67         8.94        17.98        34.92 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       30.84         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       14.56        63.42       111.78       111.91        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35         0.46        13.94        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P 
       11.90        11.11       114.15        34.88         4.21        34.68 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       12.62        11.74        18.41        85.74         4.90         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        5.36        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.30        20.38        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       12.92        47.38        52.08         8.81         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       10.78         5.98         6.41         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         0.43         9.90        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       84.72        16.24        12.16        11.84        10.65        11.05 
TCGA-QB-A6FS 
        5.79 

  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                             0                              0 
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                         82.29                         124.31 
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                         13.15                          14.60 
[1] "0.0 - 82.3 (13.2)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.1"
D15V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(11Q13.4) MUTATED    24  23
  AMP PEAK 15(11Q13.4) WILD-TYPE 118 111
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                            47                            229 
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                            23                            111 
$`AMP PEAK 15(11Q13.4) MUTATED`
TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE 
       43.43        69.90        48.76        45.11       166.52        60.23 
TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 
       24.53         3.25        66.25        13.87        35.01        12.20 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GP 
      171.55        17.92        47.54        67.43       208.04        13.91 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MM TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19L 
       21.67        61.51       167.90        53.19       148.08       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       61.05        44.05        50.89        16.37       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZB 
       46.98        33.21       210.08       216.92        48.59        48.85 
TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4F2 
       53.52        23.93       133.55       148.80        53.16        50.14 
TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
       77.88         7.23        10.13        62.79        39.58 

$`AMP PEAK 15(11Q13.4) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53       168.00        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.10       171.58        56.19        66.08       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98        46.32        86.93        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       18.38        10.03        51.68        15.06       110.93       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
        3.65         6.41        11.34         9.90        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R 
       68.09        28.60        10.49       215.44        15.68        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       17.85        45.11         3.55        52.01         6.35        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
       37.35        14.47        55.92       345.96        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        24.43        39.29        58.75       314.56       135.95 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
      101.95        14.30        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       28.83        19.76        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66        96.23       144.76       203.05        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P 
       13.02        26.37       268.93       152.35         6.44       162.08 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       31.27        32.05        92.98       174.21         4.90        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        7.00       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72       357.37        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38       101.26        74.73        11.41        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        26.73        49.45         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         2.40         9.90        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       84.72        64.44        32.48        46.36        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                          3.25                           0.16 
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                        247.04                         357.37 
  AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE 
                         50.89                          46.98 
[1] "3.2 - 247.0 (50.9)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.1"
D15V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 15(11Q13.4) MUTATED                    8             2
  AMP PEAK 15(11Q13.4) WILD-TYPE                 29             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 15(11Q13.4) MUTATED                                           6
  AMP PEAK 15(11Q13.4) WILD-TYPE                                        54
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 15(11Q13.4) MUTATED                    34
  AMP PEAK 15(11Q13.4) WILD-TYPE                 145
D15V4, multiclass
                                           clus
vv                                          AMP PEAK 15(11Q13.4) MUTATED
  DISTANT METASTASIS                                                   8
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            6
  REGIONAL LYMPH NODE                                                 34
                                           clus
vv                                          AMP PEAK 15(11Q13.4) WILD-TYPE
  DISTANT METASTASIS                                                    29
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             54
  REGIONAL LYMPH NODE                                                  145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 15(11Q13.4) MUTATED             5       1       7        1        4
  AMP PEAK 15(11Q13.4) WILD-TYPE           5       5      16        9       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 15(11Q13.4) MUTATED          3         1         3         2
  AMP PEAK 15(11Q13.4) WILD-TYPE       14         9        11         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 15(11Q13.4) MUTATED           5          2          3          6
  AMP PEAK 15(11Q13.4) WILD-TYPE        27         12         20         42
                                vv
clus                             STAGE IV
  AMP PEAK 15(11Q13.4) MUTATED          1
  AMP PEAK 15(11Q13.4) WILD-TYPE       11
D15V5, multiclass
             clus
vv            AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE
  I OR II NOS                            5                              5
  STAGE 0                                1                              5
  STAGE I                                7                             16
  STAGE IA                               1                              9
  STAGE IB                               4                             21
  STAGE II                               3                             14
  STAGE IIA                              1                              9
  STAGE IIB                              3                             11
  STAGE IIC                              2                              8
  STAGE III                              5                             27
  STAGE IIIA                             2                             12
  STAGE IIIB                             3                             20
  STAGE IIIC                             6                             42
  STAGE IV                               1                             11
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 15(11Q13.4) MUTATED       6 16  7  9
  AMP PEAK 15(11Q13.4) WILD-TYPE    47 44 48 48
D15V6, multiclass
       clus
vv      AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE
  T0+T1                            6                             47
  T2                              16                             44
  T3                               7                             48
  T4                               9                             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 15(11Q13.4) MUTATED    31   7   1   6
  AMP PEAK 15(11Q13.4) WILD-TYPE 110  44  31  31
D15V7, multiclass
    clus
vv   AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE
  N0                           31                            110
  N1                            7                             44
  N2                            1                             31
  N3                            6                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 15(11Q13.4) MUTATED    43   0   1   0   0
  AMP PEAK 15(11Q13.4) WILD-TYPE 209   4   1   2   5
D15V8, multiclass
     clus
vv    AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE
  M0                            43                            209
  M1                             0                              4
  M1A                            1                              1
  M1B                            0                              2
  M1C                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                                cls
clus                              0  1
  AMP PEAK 15(11Q13.4) MUTATED   15 13
  AMP PEAK 15(11Q13.4) WILD-TYPE 89 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.4) MUTATED     15   13
  AMP PEAK 15(11Q13.4) WILD-TYPE   89   59
     clus
vv    AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE
  NO                            15                             89
  YES                           13                             59
[1] 2 2
[1] FALSE
D15V10, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.4) MUTATED     6  44
  AMP PEAK 15(11Q13.4) WILD-TYPE  28 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.4) MUTATED      6   44
  AMP PEAK 15(11Q13.4) WILD-TYPE   28  203
     clus
vv    AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE
  NO                             6                             28
  YES                           44                            203
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.4) MUTATED    19  31
  AMP PEAK 15(11Q13.4) WILD-TYPE  89 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.4) MUTATED     19   31
  AMP PEAK 15(11Q13.4) WILD-TYPE   89  142
        clus
vv       AMP PEAK 15(11Q13.4) MUTATED AMP PEAK 15(11Q13.4) WILD-TYPE
  FEMALE                           19                             89
  MALE                             31                            142
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(11Q13.4) MUTATED       2                         0    48
  AMP PEAK 15(11Q13.4) WILD-TYPE     3                         1   227
D15V13, multiclass
                           clus
vv                          AMP PEAK 15(11Q13.4) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               48
                           clus
vv                          AMP PEAK 15(11Q13.4) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.4) MUTATED     0  50
  AMP PEAK 15(11Q13.4) WILD-TYPE   3 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.4) MUTATED      0   50
  AMP PEAK 15(11Q13.4) WILD-TYPE    3  224
                        clus
vv                       AMP PEAK 15(11Q13.4) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           50
                        clus
vv                       AMP PEAK 15(11Q13.4) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            224
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(12Q14.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(12Q14.1) MUTATED    22  26
  AMP PEAK 16(12Q14.1) WILD-TYPE 115 107
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                            48                            222 
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                            26                            107 
$`AMP PEAK 16(12Q14.1) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JN TCGA-D3-A2JO 
       16.47        70.16        22.55        10.29        56.19        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GN 
      114.67        15.25        61.38        24.00         5.39        52.01 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 
        6.97        23.11         9.90        48.79        35.80        17.56 
TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
       13.15        10.55         6.31         8.12        11.15         8.94 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-EE-A3J5 TCGA-EE-A3JE 
       39.39        47.21         8.84        27.16        21.60         0.46 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A2NE TCGA-ER-A3ET 
       12.95        25.18         3.78        28.60         1.51         6.58 
TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZK TCGA-FS-A1ZM 
        1.71         6.71        19.53        11.08        12.89        47.38 
TCGA-FS-A4F5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       28.73        31.33        16.24        15.42        12.16        14.70 

$`AMP PEAK 16(12Q14.1) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        32.42       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       81.24        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       92.42        45.11        46.98        46.32        82.29        13.32 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59        26.37        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
       95.38        47.87         1.55         4.01         2.89        11.31 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       13.22        14.60        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH 
        6.64        19.36         7.00        14.83         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
        0.00         0.00        13.22         0.20        11.57         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.09         8.84         9.99         6.48         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        34.92        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        29.65        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
        3.22        22.92        21.60        16.14        22.22        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       13.94        33.60        31.40        18.61        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       76.41         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        78.44        11.80         1.87        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       11.74         9.04        22.49        18.41        85.74         4.90 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58         5.36        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        8.22         7.17        30.87        12.92        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         3.22         7.36        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       84.72        10.13        11.84        10.65        11.05         5.79 

  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                          0.46                           0.00 
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                        114.67                         124.31 
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                        15.830                         13.745 
[1] "0.5 - 114.7 (15.8)" "0.0 - 124.3 (13.7)"
[1] "hr=" "1.1"
D16V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(12Q14.1) MUTATED    23  26
  AMP PEAK 16(12Q14.1) WILD-TYPE 119 108
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                            49                            227 
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                            26                            108 
$`AMP PEAK 16(12Q14.1) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JN TCGA-D3-A2JO 
       16.57        71.80        31.59        43.43        56.19        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GN 
      130.72        58.06        86.93        24.53        21.47       135.75 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 
        7.43       125.19         9.90        48.89        36.03       215.44 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A29D 
       13.87         3.55        27.22         8.65        94.98        13.97 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-EE-A3J5 
       58.75        47.54       208.04        21.67       136.47        36.95 
TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A2NE 
       33.40        13.94        98.40        48.89        61.05        20.15 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZK 
       80.32        33.21       210.08        40.27        15.45        23.93 
TCGA-FS-A1ZM TCGA-FS-A4F5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      101.26        28.73       117.93        64.44        62.79        32.48 
TCGA-GN-A26D 
       39.58 

$`AMP PEAK 16(12Q14.1) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04       112.57       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
      171.58        45.11        46.98        46.32       166.52        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        39.75       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      110.93       137.92       166.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        6.41        11.34         3.25        25.18        66.25        22.95 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       10.49        15.68        10.16        17.85        45.11        35.01 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       52.01         6.35        12.20        29.82        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      168.26        13.55        63.35        80.61        47.84        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       37.35        14.47        55.92       345.96        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
       17.92        46.82       102.90        24.43        39.29        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      103.56        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JH 
      127.20        64.08        34.32        53.19        27.35       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      148.08        31.40        35.44        50.76         9.17        77.75 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      131.51        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        43.82        23.34        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
      247.04        46.98        92.98       174.21         4.90        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        7.00       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        32.75        47.38        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
        2.40         9.90         7.23        14.04       120.46        84.72 
TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       10.13        46.36        12.62       294.77         6.67 

  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                          3.55                           0.16 
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                        215.44                         357.37 
  AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE 
                         43.43                          48.59 
[1] "3.5 - 215.4 (43.4)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.3"
D16V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 16(12Q14.1) MUTATED                    5             1
  AMP PEAK 16(12Q14.1) WILD-TYPE                 32             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 16(12Q14.1) MUTATED                                          13
  AMP PEAK 16(12Q14.1) WILD-TYPE                                        47
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 16(12Q14.1) MUTATED                    30
  AMP PEAK 16(12Q14.1) WILD-TYPE                 149
D16V4, multiclass
                                           clus
vv                                          AMP PEAK 16(12Q14.1) MUTATED
  DISTANT METASTASIS                                                   5
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           13
  REGIONAL LYMPH NODE                                                 30
                                           clus
vv                                          AMP PEAK 16(12Q14.1) WILD-TYPE
  DISTANT METASTASIS                                                    32
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             47
  REGIONAL LYMPH NODE                                                  149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 16(12Q14.1) MUTATED             1       1       5        1        4
  AMP PEAK 16(12Q14.1) WILD-TYPE           9       5      18        9       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 16(12Q14.1) MUTATED          2         0         4         4
  AMP PEAK 16(12Q14.1) WILD-TYPE       15        10        10         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 16(12Q14.1) MUTATED           6          4          8          6
  AMP PEAK 16(12Q14.1) WILD-TYPE        26         10         15         42
                                vv
clus                             STAGE IV
  AMP PEAK 16(12Q14.1) MUTATED          2
  AMP PEAK 16(12Q14.1) WILD-TYPE       10
D16V5, multiclass
             clus
vv            AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE
  I OR II NOS                            1                              9
  STAGE 0                                1                              5
  STAGE I                                5                             18
  STAGE IA                               1                              9
  STAGE IB                               4                             21
  STAGE II                               2                             15
  STAGE IIA                              0                             10
  STAGE IIB                              4                             10
  STAGE IIC                              4                              6
  STAGE III                              6                             26
  STAGE IIIA                             4                             10
  STAGE IIIB                             8                             15
  STAGE IIIC                             6                             42
  STAGE IV                               2                             10
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 16(12Q14.1) MUTATED      10  9  9 15
  AMP PEAK 16(12Q14.1) WILD-TYPE    43 51 46 42
D16V6, multiclass
       clus
vv      AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE
  T0+T1                           10                             43
  T2                               9                             51
  T3                               9                             46
  T4                              15                             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 16(12Q14.1) MUTATED    24  15   4   5
  AMP PEAK 16(12Q14.1) WILD-TYPE 117  36  28  32
D16V7, multiclass
    clus
vv   AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE
  N0                           24                            117
  N1                           15                             36
  N2                            4                             28
  N3                            5                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 16(12Q14.1) MUTATED    46   0   1   0   1
  AMP PEAK 16(12Q14.1) WILD-TYPE 206   4   1   2   4
D16V8, multiclass
     clus
vv    AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE
  M0                            46                            206
  M1                             0                              4
  M1A                            1                              1
  M1B                            0                              2
  M1C                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                                cls
clus                              0  1
  AMP PEAK 16(12Q14.1) MUTATED   21 16
  AMP PEAK 16(12Q14.1) WILD-TYPE 83 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(12Q14.1) MUTATED     21   16
  AMP PEAK 16(12Q14.1) WILD-TYPE   83   56
     clus
vv    AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE
  NO                            21                             83
  YES                           16                             56
[1] 2 2
[1] FALSE
D16V10, binary
                                cls
clus                               0   1
  AMP PEAK 16(12Q14.1) MUTATED     2  48
  AMP PEAK 16(12Q14.1) WILD-TYPE  32 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(12Q14.1) MUTATED      2   48
  AMP PEAK 16(12Q14.1) WILD-TYPE   32  199
     clus
vv    AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE
  NO                             2                             32
  YES                           48                            199
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, binary
                                cls
clus                               0   1
  AMP PEAK 16(12Q14.1) MUTATED    20  30
  AMP PEAK 16(12Q14.1) WILD-TYPE  88 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(12Q14.1) MUTATED     20   30
  AMP PEAK 16(12Q14.1) WILD-TYPE   88  143
        clus
vv       AMP PEAK 16(12Q14.1) MUTATED AMP PEAK 16(12Q14.1) WILD-TYPE
  FEMALE                           20                             88
  MALE                             30                            143
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12Q14.1) MUTATED       2                         0    48
  AMP PEAK 16(12Q14.1) WILD-TYPE     3                         1   227
D16V13, multiclass
                           clus
vv                          AMP PEAK 16(12Q14.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               48
                           clus
vv                          AMP PEAK 16(12Q14.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                                cls
clus                               0   1
  AMP PEAK 16(12Q14.1) MUTATED     1  48
  AMP PEAK 16(12Q14.1) WILD-TYPE   2 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(12Q14.1) MUTATED      1   48
  AMP PEAK 16(12Q14.1) WILD-TYPE    2  226
                        clus
vv                       AMP PEAK 16(12Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           48
                        clus
vv                       AMP PEAK 16(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            226
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(12Q15) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(12Q15) MUTATED    22  24
  AMP PEAK 17(12Q15) WILD-TYPE 115 109
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          46                          224 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          24                          109 
$`AMP PEAK 17(12Q15) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       16.47        70.16        22.55        56.19        64.44       114.67 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51H TCGA-D3-A5GL 
       15.25        61.38        24.00         5.39        15.09        95.38 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       52.01         6.97        23.11        13.22        48.79        35.80 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.56        10.55         8.12        11.15         8.94        39.39 
TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI 
       47.21         8.84        27.16        21.60         0.46        33.60 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       31.40        12.95        25.18         3.78       114.15        34.88 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F5 
        1.51         6.58        12.89        47.38         8.65        28.73 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       16.24        15.42        12.16        14.70 

$`AMP PEAK 17(12Q15) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        32.42       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        69.90        11.41        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
        6.31        92.42        45.11        46.98        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       13.32         6.31         9.34       103.59        26.37        80.22 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       42.71        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       47.87         1.55         4.01         2.89         9.90        11.31 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       14.60        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       19.36         7.00        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
        0.00         0.00        13.22         0.20        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        38.63         8.55         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.50        12.03         8.09         8.84         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
        9.67        34.29        17.98        34.92        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        21.60        29.65        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       27.35        13.94        18.61        38.40         5.72        76.41 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        3.52        11.90        11.11         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       11.80         1.87        13.08        12.62        11.74         9.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       22.49         1.71        18.41        85.74         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58         5.36        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       52.08         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
        0.82         5.23        53.85         3.22         7.36        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 
       24.85        31.33        84.72        10.13        11.84        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                        0.46                         0.00 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                      114.67                       124.31 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                      19.580                       13.185 
[1] "0.5 - 114.7 (19.6)" "0.0 - 124.3 (13.2)"
[1] "hr=" "1.2"
D17V2, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(12Q15) MUTATED    23  24
  AMP PEAK 17(12Q15) WILD-TYPE 119 110
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          47                          229 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          24                          110 
$`AMP PEAK 17(12Q15) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       16.57        71.80        31.59        56.19        66.08       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51H TCGA-D3-A5GL 
       58.06        86.93        24.53        21.47        40.14       110.93 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
      135.75         7.43       125.19        66.25        48.89        36.03 
TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
      215.44         3.55        27.22        94.98        13.97        58.75 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-EE-A3J5 TCGA-EE-A3JE 
       47.54       208.04        21.67       136.47        36.95        33.40 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G 
      148.08        31.40        13.94        98.40        48.89       268.93 
TCGA-ER-A19H TCGA-ER-A2NE TCGA-ER-A3ET TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      152.35        20.15        80.32        23.93       101.26       133.55 
TCGA-FS-A4F5 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       28.73        64.44        62.79        32.48        39.58 

$`AMP PEAK 17(12Q15) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04       112.57       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        69.90        11.87        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       12.10       171.58        45.11        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       60.23        13.87         9.34       103.59        39.75       161.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       43.69       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      137.92       166.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY 
       11.34         3.25         9.90        25.18        22.95       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        45.11        35.01 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       52.01         6.35        12.20        29.82         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        37.35        14.47        55.92       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       135.95        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       103.56        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      172.18       127.20        64.08        34.32        53.19        27.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
      101.79        35.44        50.76         9.17        77.75        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       13.02        26.37         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       23.34        16.37        31.27        32.05       247.04        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       33.21        92.98       174.21         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        7.00       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       40.27        15.45         9.70        32.75        47.38        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      117.93        84.72        10.13        46.36        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                        3.55                         0.16 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                      268.93                       357.37 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                       56.19                        47.38 
[1] "3.5 - 268.9 (56.2)" "0.2 - 357.4 (47.4)"
[1] "hr=" "1"  
D17V3, continuous
                              vv
clus                           DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 17(12Q15) MUTATED                    4             1
  AMP PEAK 17(12Q15) WILD-TYPE                 33             3
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 17(12Q15) MUTATED                                          13
  AMP PEAK 17(12Q15) WILD-TYPE                                        47
                              vv
clus                           REGIONAL LYMPH NODE
  AMP PEAK 17(12Q15) MUTATED                    29
  AMP PEAK 17(12Q15) WILD-TYPE                 150
D17V4, multiclass
                                           clus
vv                                          AMP PEAK 17(12Q15) MUTATED
  DISTANT METASTASIS                                                 4
  PRIMARY TUMOR                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                         13
  REGIONAL LYMPH NODE                                               29
                                           clus
vv                                          AMP PEAK 17(12Q15) WILD-TYPE
  DISTANT METASTASIS                                                  33
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           47
  REGIONAL LYMPH NODE                                                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 17(12Q15) MUTATED             2       1       5        1        4
  AMP PEAK 17(12Q15) WILD-TYPE           8       5      18        9       21
                              vv
clus                           STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 17(12Q15) MUTATED          2         0         3         2         6
  AMP PEAK 17(12Q15) WILD-TYPE       15        10        11         8        26
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 17(12Q15) MUTATED            4          8          6        1
  AMP PEAK 17(12Q15) WILD-TYPE         10         15         42       11
D17V5, multiclass
             clus
vv            AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  I OR II NOS                          2                            8
  STAGE 0                              1                            5
  STAGE I                              5                           18
  STAGE IA                             1                            9
  STAGE IB                             4                           21
  STAGE II                             2                           15
  STAGE IIA                            0                           10
  STAGE IIB                            3                           11
  STAGE IIC                            2                            8
  STAGE III                            6                           26
  STAGE IIIA                           4                           10
  STAGE IIIB                           8                           15
  STAGE IIIC                           6                           42
  STAGE IV                             1                           11
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 17(12Q15) MUTATED      10 10  8 12
  AMP PEAK 17(12Q15) WILD-TYPE    43 50 47 45
D17V6, multiclass
       clus
vv      AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  T0+T1                         10                           43
  T2                            10                           50
  T3                             8                           47
  T4                            12                           45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 17(12Q15) MUTATED    23  15   4   5
  AMP PEAK 17(12Q15) WILD-TYPE 118  36  28  32
D17V7, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  N0                         23                          118
  N1                         15                           36
  N2                          4                           28
  N3                          5                           32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B M1C
  AMP PEAK 17(12Q15) MUTATED    46   0   0   0   1
  AMP PEAK 17(12Q15) WILD-TYPE 206   4   2   2   4
D17V8, multiclass
     clus
vv    AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  M0                          46                          206
  M1                           0                            4
  M1A                          0                            2
  M1B                          0                            2
  M1C                          1                            4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                              cls
clus                            0  1
  AMP PEAK 17(12Q15) MUTATED   21 12
  AMP PEAK 17(12Q15) WILD-TYPE 83 60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED     21   12
  AMP PEAK 17(12Q15) WILD-TYPE   83   60
     clus
vv    AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  NO                          21                           83
  YES                         12                           60
[1] 2 2
[1] FALSE
D17V10, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED     2  46
  AMP PEAK 17(12Q15) WILD-TYPE  32 201
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED      2   46
  AMP PEAK 17(12Q15) WILD-TYPE   32  201
     clus
vv    AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  NO                           2                           32
  YES                         46                          201
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED    18  30
  AMP PEAK 17(12Q15) WILD-TYPE  90 143
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED     18   30
  AMP PEAK 17(12Q15) WILD-TYPE   90  143
        clus
vv       AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  FEMALE                         18                           90
  MALE                           30                          143
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(12Q15) MUTATED       1                         0    47
  AMP PEAK 17(12Q15) WILD-TYPE     4                         1   228
D17V13, multiclass
                           clus
vv                          AMP PEAK 17(12Q15) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             47
                           clus
vv                          AMP PEAK 17(12Q15) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED     1  46
  AMP PEAK 17(12Q15) WILD-TYPE   2 228
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED      1   46
  AMP PEAK 17(12Q15) WILD-TYPE    2  228
                        clus
vv                       AMP PEAK 17(12Q15) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         46
                        clus
vv                       AMP PEAK 17(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          228
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(13Q12.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(13Q12.3) MUTATED    34  42
  AMP PEAK 18(13Q12.3) WILD-TYPE 103  91
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                            76                            194 
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                            42                             91 
$`AMP PEAK 18(13Q12.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3C6 
       16.47         8.52        70.16        30.87        45.11        15.25 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       61.38        13.32        13.94        47.87         1.55        23.11 
TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A17Y 
       35.80        36.69         7.00         0.20         0.13        10.55 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
        8.12         5.13        36.07         9.21         7.99         9.90 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T 
       38.63         8.55         1.08        12.03         8.84         6.48 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
        9.67        39.39        47.21        28.31        33.83         5.42 
TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 
        2.70        26.99       124.31        13.81         3.22        21.60 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       22.22        33.60        12.95         5.72         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NC 
       11.90        13.45        28.60        42.84        34.68        11.80 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 
        6.58         1.71         4.90         6.71         3.45        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
       14.24        15.52         7.33        19.53        12.92         8.65 
TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A265 
       40.64         0.82         3.22         2.27         0.13        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-OD-A75X 
       16.24        15.42        10.65        11.05 

$`AMP PEAK 18(13Q12.3) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      111.09        32.42       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        69.90        11.41         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       92.42        56.19        64.44       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       82.29        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D9-A3Z1 
        8.84        20.48        95.38        52.01         6.97         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        2.89         9.90        11.31        13.22        14.60        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       25.15         4.93        22.36         6.64        19.36        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       14.83        13.15         0.00         0.00        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        12.20         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
        4.34         5.13         1.18        37.97        11.15         4.41 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       27.12         9.50         8.09         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC 
        8.09        11.31        49.22        23.90         8.94        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        30.08        19.43        16.01        35.54 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       30.84         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       98.27         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84         3.68        30.15        15.95        12.72 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       22.92        21.60        16.14        27.35         0.46        13.94 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F 
       31.40        18.61        38.40        76.41        25.18        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      114.15        34.88         4.21         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 
        9.04        22.49        18.41        85.74         3.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       64.47        11.01         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.89        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
        8.81        49.15         8.68        27.39         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.99         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
       12.85        24.85        31.33        10.13        12.16        14.70 
TCGA-GN-A4U8 TCGA-QB-A6FS 
       11.84         5.79 

  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                          0.13                           0.00 
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                        124.31                         122.73 
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                        12.475                         15.520 
[1] "0.1 - 124.3 (12.5)" "0.0 - 122.7 (15.5)"
[1] "hr=" "1.5"
D18V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(13Q12.3) MUTATED    36  42
  AMP PEAK 18(13Q12.3) WILD-TYPE 106  92
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                            78                            198 
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                            42                             92 
$`AMP PEAK 18(13Q12.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3C6 
       16.57        16.67        71.80        48.76        45.11        58.06 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       86.93        60.23        15.06       137.92       166.19       125.19 
TCGA-D9-A149 TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5KH 
       54.67        36.03        61.18        10.49        10.16        17.85 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H 
        3.55        27.22        94.98        68.15       109.64       168.26 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P 
       63.35        80.61        39.62        72.07         2.60        56.42 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM 
       14.47       345.96        39.29        47.54       208.04        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF 
       90.97        13.91        28.83       248.65       124.31        13.81 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
      172.18        64.08        53.19       148.08        13.94         9.17 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       48.89        12.59        13.02       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 
      162.08        43.82        80.32        33.21         4.90       210.08 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE 
       48.59       202.65        20.91        28.08         7.79        40.27 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD 
       47.38       133.55        53.16        27.09        50.14        77.88 
TCGA-FW-A3TU TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-OD-A75X 
       47.54        84.72        64.44        62.79        12.62       294.77 

$`AMP PEAK 18(13Q12.3) WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.04       112.57       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        69.90        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        56.19        66.08       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D9-A148 
       10.03        51.68       110.93       135.75         7.43       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        22.95        48.89       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55        35.93       107.34        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG 
       68.09        28.60       215.44        15.68        13.87        45.11 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       35.01        52.01         6.35        12.20        29.82         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       33.73        14.70        26.89         4.96       151.27        78.87 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.55        47.84        13.97        32.19        44.35        18.61 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        55.92        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        24.43        58.75        67.43       314.56       135.95 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GR 
       48.72        89.33        54.74        79.66       101.95        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
       55.59        44.88        94.82        21.67       129.27        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       144.76       203.05       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      103.56       136.47        41.59        53.26       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        54.51        23.47       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       34.32        27.35        33.40       101.79        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       50.76        77.75        98.40        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
        6.44        50.89        37.25       148.18        79.99        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       20.15        16.37        31.27        32.05       247.04        46.98 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY 
       92.98       174.21        15.16         7.00       216.92       228.59 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        53.52        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        23.93       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
      174.84        12.43        26.73        49.45         0.20        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
      117.93        10.13        32.48        39.58        46.36         6.67 

  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                          2.60                           0.16 
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                        345.96                         357.37 
  AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE 
                        53.175                         46.590 
[1] "2.6 - 346.0 (53.2)" "0.2 - 357.4 (46.6)"
[1] "hr=" "1.1"
D18V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 18(13Q12.3) MUTATED                   16             0
  AMP PEAK 18(13Q12.3) WILD-TYPE                 21             4
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 18(13Q12.3) MUTATED                                          19
  AMP PEAK 18(13Q12.3) WILD-TYPE                                        41
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 18(13Q12.3) MUTATED                    44
  AMP PEAK 18(13Q12.3) WILD-TYPE                 135
D18V4, multiclass
                                           clus
vv                                          AMP PEAK 18(13Q12.3) MUTATED
  DISTANT METASTASIS                                                  16
  PRIMARY TUMOR                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           19
  REGIONAL LYMPH NODE                                                 44
                                           clus
vv                                          AMP PEAK 18(13Q12.3) WILD-TYPE
  DISTANT METASTASIS                                                    21
  PRIMARY TUMOR                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             41
  REGIONAL LYMPH NODE                                                  135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 18(13Q12.3) MUTATED             2       1      10        2       10
  AMP PEAK 18(13Q12.3) WILD-TYPE           8       5      13        8       15
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 18(13Q12.3) MUTATED          3         1         3         6
  AMP PEAK 18(13Q12.3) WILD-TYPE       14         9        11         4
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 18(13Q12.3) MUTATED           8          4          9         11
  AMP PEAK 18(13Q12.3) WILD-TYPE        24         10         14         37
                                vv
clus                             STAGE IV
  AMP PEAK 18(13Q12.3) MUTATED          2
  AMP PEAK 18(13Q12.3) WILD-TYPE       10
D18V5, multiclass
             clus
vv            AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE
  I OR II NOS                            2                              8
  STAGE 0                                1                              5
  STAGE I                               10                             13
  STAGE IA                               2                              8
  STAGE IB                              10                             15
  STAGE II                               3                             14
  STAGE IIA                              1                              9
  STAGE IIB                              3                             11
  STAGE IIC                              6                              4
  STAGE III                              8                             24
  STAGE IIIA                             4                             10
  STAGE IIIB                             9                             14
  STAGE IIIC                            11                             37
  STAGE IV                               2                             10
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 18(13Q12.3) MUTATED      15 22 10 18
  AMP PEAK 18(13Q12.3) WILD-TYPE    38 38 45 39
D18V6, multiclass
       clus
vv      AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE
  T0+T1                           15                             38
  T2                              22                             38
  T3                              10                             45
  T4                              18                             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 18(13Q12.3) MUTATED    41  20   4   8
  AMP PEAK 18(13Q12.3) WILD-TYPE 100  31  28  29
D18V7, multiclass
    clus
vv   AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE
  N0                           41                            100
  N1                           20                             31
  N2                            4                             28
  N3                            8                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 18(13Q12.3) MUTATED    73   1   1   0   0
  AMP PEAK 18(13Q12.3) WILD-TYPE 179   3   1   2   5
D18V8, multiclass
     clus
vv    AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE
  M0                            73                            179
  M1                             1                              3
  M1A                            1                              1
  M1B                            0                              2
  M1C                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                                cls
clus                              0  1
  AMP PEAK 18(13Q12.3) MUTATED   26 21
  AMP PEAK 18(13Q12.3) WILD-TYPE 78 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q12.3) MUTATED     26   21
  AMP PEAK 18(13Q12.3) WILD-TYPE   78   51
     clus
vv    AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE
  NO                            26                             78
  YES                           21                             51
[1] 2 2
[1] FALSE
D18V10, binary
                                cls
clus                               0   1
  AMP PEAK 18(13Q12.3) MUTATED    10  70
  AMP PEAK 18(13Q12.3) WILD-TYPE  24 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q12.3) MUTATED     10   70
  AMP PEAK 18(13Q12.3) WILD-TYPE   24  177
     clus
vv    AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE
  NO                            10                             24
  YES                           70                            177
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, binary
                                cls
clus                               0   1
  AMP PEAK 18(13Q12.3) MUTATED    31  49
  AMP PEAK 18(13Q12.3) WILD-TYPE  77 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q12.3) MUTATED     31   49
  AMP PEAK 18(13Q12.3) WILD-TYPE   77  124
        clus
vv       AMP PEAK 18(13Q12.3) MUTATED AMP PEAK 18(13Q12.3) WILD-TYPE
  FEMALE                           31                             77
  MALE                             49                            124
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(13Q12.3) MUTATED       3                         0    77
  AMP PEAK 18(13Q12.3) WILD-TYPE     2                         1   198
D18V13, multiclass
                           clus
vv                          AMP PEAK 18(13Q12.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               77
                           clus
vv                          AMP PEAK 18(13Q12.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                                cls
clus                               0   1
  AMP PEAK 18(13Q12.3) MUTATED     0  78
  AMP PEAK 18(13Q12.3) WILD-TYPE   3 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q12.3) MUTATED      0   78
  AMP PEAK 18(13Q12.3) WILD-TYPE    3  196
                        clus
vv                       AMP PEAK 18(13Q12.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       AMP PEAK 18(13Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            196
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(15Q26.2) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 19(15Q26.2) MUTATED   46 42
  AMP PEAK 19(15Q26.2) WILD-TYPE 91 91
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                            88                            182 
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                            42                             91 
$`AMP PEAK 19(15Q26.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       32.42        22.55        21.14        88.50        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MU 
       30.87        92.42        56.19        82.29        13.32        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        5.39        80.22        17.72         2.89         9.90        11.31 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       48.79        35.80        36.69         7.00        17.56        13.15 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       10.55         8.12        12.20        36.07         5.13         9.21 
TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2GH 
       11.15         6.48         8.68         8.09        49.22        47.21 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
       30.08        28.31        33.83        30.84         5.42        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP 
       98.27         2.70         9.53        63.42        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE 
       21.60        29.65        27.16       124.31       122.73        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3JH TCGA-EE-A3JI 
       13.81        15.95         3.22        21.60        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S 
       31.40         3.78         3.52        28.60        34.68        36.07 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 
        6.58        22.49        85.74         4.90         6.71         5.36 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       14.24         7.33        20.38         8.22        12.92        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GF-A4EO 
        8.65         0.82         3.22         2.27         0.99         7.23 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       31.33        84.72        16.24        12.16 

$`AMP PEAK 19(15Q26.2) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        70.16       110.79        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB 
       45.83        81.24        10.29        85.32         8.38        68.22 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       15.25        46.98        46.32        61.38        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
        9.34       103.59        42.71        15.09        41.10         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       20.48        13.94        95.38        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
        6.97        23.11         4.01        13.22        14.60        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       10.03        39.19        13.68         9.99        44.52        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44R 
        4.93        22.36         6.64        19.36        14.83         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13         0.00         0.00        13.22         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        6.31         1.12         1.35         5.13         4.31         4.34 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.84         9.99         2.43        11.31        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
        8.94        39.39        34.29        17.98        34.92        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       16.01        35.54         1.15        13.02        34.98         8.84 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
      111.78       111.91        56.02        23.05         5.56        25.84 
TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.68        12.72        22.92        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       27.35         0.46        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       76.41        25.18        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
        4.21        13.45        42.84         9.57        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX 
        9.04         1.71        18.41         3.58        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE 
       11.01        23.80        15.52         7.30         3.39        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR 
       11.08         7.17        30.87        12.89        47.38         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
       49.15        40.64         8.68        27.39         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
        0.20         0.13         0.16         0.43         9.90        12.85 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       24.85        10.13        15.42        14.70        11.84        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                          0.82                           0.00 
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                        124.31                         114.67 
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                         19.05                          13.15 
[1] "0.8 - 124.3 (19.0)" "0.0 - 114.7 (13.2)"
[1] "hr=" "1.2"
D19V2, survival
                                sevent
clus2                             0  1
  AMP PEAK 19(15Q26.2) MUTATED   48 42
  AMP PEAK 19(15Q26.2) WILD-TYPE 94 92
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                            90                            186 
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                            42                             92 
$`AMP PEAK 19(15Q26.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      112.57        31.59        23.77       115.53        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MU 
       48.76       171.58        56.19       166.52        60.23        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
       21.47       161.85        18.38       151.53        54.67         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F3 
        9.90        25.18        48.89        36.03        61.18        10.49 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20B 
      215.44        13.87        27.22        94.98        26.89       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       78.87       168.26        13.97       345.96       171.55        17.92 
TCGA-EE-A2A1 TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      102.90       208.04        48.72        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MJ 
       13.91        94.82       129.27        28.83        47.28        96.23 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
       47.54       248.65        43.23       103.56       136.47       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
      122.73        54.51        13.81        23.47       172.18        36.95 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19M 
      101.79       148.08        31.40        48.89        12.59        61.05 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P 
      162.08        37.25        80.32        46.98       174.21         4.90 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      210.08         7.00        20.91         7.79       357.37        53.52 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD 
       47.38        74.73       133.55        27.09        50.14        77.88 
TCGA-FW-A3R5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       22.92         7.23       117.93        84.72        64.44        32.48 

$`AMP PEAK 19(15Q26.2) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB 
       90.90        95.74        43.43       103.10        65.49       168.00 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98        46.32        86.93        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
        9.34       103.59        43.69        40.14       131.90        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       51.68        15.06       110.93       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6EC 
        7.43       125.19         3.65         6.41        11.34        66.25 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        10.16        17.85        45.11        35.01         3.55 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       52.01         6.35        12.20        29.82         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A 
       14.70        68.15         4.96       151.27        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       25.87        46.82        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       314.56       135.95        89.33        54.74        79.66 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       14.30        55.59        44.88        21.67        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AH 
      167.90        41.59        53.26        25.84         3.68       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        64.08        34.32        53.19        27.35        33.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       44.05        50.89       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL 
       20.15        16.37        31.27        32.05       247.04        33.21 
TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       92.98        15.16       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       28.08        27.72        48.85        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       32.75        23.93       101.26        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU 
      174.84        12.43        26.73        49.45         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
        0.16         2.40         9.90        14.04       120.46        10.13 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        39.58        46.36        12.62       294.77         6.67 

  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                          3.25                           0.16 
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                        357.37                         314.56 
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                        55.430                         44.995 
[1] "3.2 - 357.4 (55.4)" "0.2 - 314.6 (45.0)"
[1] "hr=" "1.3"
D19V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 19(15Q26.2) MUTATED                    9             2
  AMP PEAK 19(15Q26.2) WILD-TYPE                 28             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 19(15Q26.2) MUTATED                                          18
  AMP PEAK 19(15Q26.2) WILD-TYPE                                        42
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 19(15Q26.2) MUTATED                    64
  AMP PEAK 19(15Q26.2) WILD-TYPE                 115
D19V4, multiclass
                                           clus
vv                                          AMP PEAK 19(15Q26.2) MUTATED
  DISTANT METASTASIS                                                   9
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           18
  REGIONAL LYMPH NODE                                                 64
                                           clus
vv                                          AMP PEAK 19(15Q26.2) WILD-TYPE
  DISTANT METASTASIS                                                    28
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             42
  REGIONAL LYMPH NODE                                                  115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 19(15Q26.2) MUTATED             9       2      11        4        6
  AMP PEAK 19(15Q26.2) WILD-TYPE           1       4      12        6       19
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 19(15Q26.2) MUTATED          7         2         2         2
  AMP PEAK 19(15Q26.2) WILD-TYPE       10         8        12         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 19(15Q26.2) MUTATED          11          7         10         11
  AMP PEAK 19(15Q26.2) WILD-TYPE        21          7         13         37
                                vv
clus                             STAGE IV
  AMP PEAK 19(15Q26.2) MUTATED          1
  AMP PEAK 19(15Q26.2) WILD-TYPE       11
D19V5, multiclass
             clus
vv            AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE
  I OR II NOS                            9                              1
  STAGE 0                                2                              4
  STAGE I                               11                             12
  STAGE IA                               4                              6
  STAGE IB                               6                             19
  STAGE II                               7                             10
  STAGE IIA                              2                              8
  STAGE IIB                              2                             12
  STAGE IIC                              2                              8
  STAGE III                             11                             21
  STAGE IIIA                             7                              7
  STAGE IIIB                            10                             13
  STAGE IIIC                            11                             37
  STAGE IV                               1                             11
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 19(15Q26.2) MUTATED      19 22 18 13
  AMP PEAK 19(15Q26.2) WILD-TYPE    34 38 37 44
D19V6, multiclass
       clus
vv      AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE
  T0+T1                           19                             34
  T2                              22                             38
  T3                              18                             37
  T4                              13                             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 19(15Q26.2) MUTATED   49 17 12  9
  AMP PEAK 19(15Q26.2) WILD-TYPE 92 34 20 28
D19V7, multiclass
    clus
vv   AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE
  N0                           49                             92
  N1                           17                             34
  N2                           12                             20
  N3                            9                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 19(15Q26.2) MUTATED    86   1   0   1   0
  AMP PEAK 19(15Q26.2) WILD-TYPE 166   3   2   1   5
D19V8, multiclass
     clus
vv    AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE
  M0                            86                            166
  M1                             1                              3
  M1A                            0                              2
  M1B                            1                              1
  M1C                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                                cls
clus                              0  1
  AMP PEAK 19(15Q26.2) MUTATED   34 16
  AMP PEAK 19(15Q26.2) WILD-TYPE 70 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.2) MUTATED     34   16
  AMP PEAK 19(15Q26.2) WILD-TYPE   70   56
     clus
vv    AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE
  NO                            34                             70
  YES                           16                             56
[1] 2 2
[1] FALSE
D19V10, binary
                                cls
clus                               0   1
  AMP PEAK 19(15Q26.2) MUTATED    15  78
  AMP PEAK 19(15Q26.2) WILD-TYPE  19 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.2) MUTATED     15   78
  AMP PEAK 19(15Q26.2) WILD-TYPE   19  169
     clus
vv    AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE
  NO                            15                             19
  YES                           78                            169
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, binary
                                cls
clus                               0   1
  AMP PEAK 19(15Q26.2) MUTATED    37  56
  AMP PEAK 19(15Q26.2) WILD-TYPE  71 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.2) MUTATED     37   56
  AMP PEAK 19(15Q26.2) WILD-TYPE   71  117
        clus
vv       AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE
  FEMALE                           37                             71
  MALE                             56                            117
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(15Q26.2) MUTATED       2                         0    91
  AMP PEAK 19(15Q26.2) WILD-TYPE     3                         1   184
D19V13, multiclass
                           clus
vv                          AMP PEAK 19(15Q26.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               91
                           clus
vv                          AMP PEAK 19(15Q26.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                                cls
clus                               0   1
  AMP PEAK 19(15Q26.2) MUTATED     1  91
  AMP PEAK 19(15Q26.2) WILD-TYPE   2 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.2) MUTATED      1   91
  AMP PEAK 19(15Q26.2) WILD-TYPE    2  183
                        clus
vv                       AMP PEAK 19(15Q26.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           91
                        clus
vv                       AMP PEAK 19(15Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            183
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(17Q25.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(17Q25.3) MUTATED   48 44
  AMP PEAK 20(17Q25.3) WILD-TYPE 89 89
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                            92                            178 
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                            44                             89 
$`AMP PEAK 20(17Q25.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB 
       16.47         8.52       111.09        22.55        45.83        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 
       69.90        11.41        30.87        92.42       114.67        15.25 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51T 
       61.38        24.00         9.34         5.39         8.84        13.94 
TCGA-D3-A5GS TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 
        6.97         9.90        48.79        51.12        39.19        36.69 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EE-A17Y 
        4.93         6.64         7.00        17.56         0.20        10.55 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H 
        1.12         1.35         5.13         4.31         5.13         9.21 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       11.15         4.41         1.08         9.50        12.03         8.84 
TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI 
        2.43         8.94        39.39        34.29        47.21        30.08 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MH 
       28.31         5.42         1.15         2.70         9.53         7.96 
TCGA-EE-A2MI TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       14.56        25.08        26.99        29.65        27.16        23.05 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
       25.84        30.15        21.60        22.22        13.94        33.60 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NC 
        3.78        11.11        42.84         9.57        17.72        11.80 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U9 
        1.51         6.58        22.49         1.71        18.41         5.36 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       64.47         3.45         8.22        12.89        47.38         8.65 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A268 
       40.64         8.68         2.27         0.20        84.72        15.42 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

$`AMP PEAK 20(17Q25.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
       32.42        70.16       110.79        28.08        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH 
       85.32         8.38        21.14        88.50         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 
        6.31        56.19        64.44        45.11        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       82.29        13.32         6.31       103.59        26.37        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
       42.71        15.09        41.10        17.72        20.48        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87         1.55        23.11         4.01         2.89 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 
       11.31        13.22        14.60        35.80        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
        9.99        44.52        25.15        22.36        19.36        14.83 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       13.15         0.13         0.00         0.00        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C 
       11.57         6.31         8.12        12.20        36.07         4.34 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        38.63         8.55 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       27.12         8.09         9.99         6.48         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE 
       11.31        49.22        23.90         9.67        17.98        34.92 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS 
       19.43        16.01        35.54        33.83        30.84        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       34.98        36.33         8.84        98.27         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       29.46        44.25        63.42       111.78       111.91        56.02 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       21.60         5.56       124.31       122.73         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35         0.46        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
        5.72        76.41        25.18         3.52        11.90       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S 
       34.88         4.21        13.45        28.60        34.68        36.07 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       78.44         1.87        13.08        12.62        11.74         9.04 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90         6.71         3.58        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       19.53        11.08         7.17        30.87        12.92        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
        8.81        49.15        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        3.22         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        7.23        12.85        24.85        31.33        10.13        16.24 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       12.16        11.84        10.65        11.05 

  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                           0.2                            0.0 
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                        114.67                         124.31 
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                        12.460                         14.715 
[1] "0.2 - 114.7 (12.5)" "0.0 - 124.3 (14.7)"
[1] "hr=" "1.1"
D20V2, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(17Q25.3) MUTATED   51 44
  AMP PEAK 20(17Q25.3) WILD-TYPE 91 90
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                            95                            181 
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                            44                             90 
$`AMP PEAK 20(17Q25.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB 
       16.57        16.67       112.04        31.59        90.90       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 
       69.90        11.87        48.76       171.58       130.72        58.06 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51T 
       86.93        24.53         9.34        21.47        10.03        15.06 
TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HY 
        7.43       151.53         3.65         9.90        48.89       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 
      194.83        61.18        65.92        68.09        10.49       215.44 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       10.16         3.55        27.22        33.73        14.70        68.15 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
        4.96        78.87       168.26        13.97        32.19         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GB 
       18.61        56.42        14.47        25.87        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR 
       67.43       208.04        48.72        75.48        13.91        14.30 
TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MN TCGA-EE-A2MP 
       28.83        47.28        16.96       204.66        47.54       248.65 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 
      103.56       136.47        41.59        25.84        54.51        36.95 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19N 
       53.19       101.79       148.08        48.89        26.37        44.05 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A3EV 
       50.89       148.18        43.82        20.15        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZD 
       33.21        92.98         7.00       216.92        48.59        53.52 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4FD 
       23.93       101.26       133.55        53.16        26.56        77.88 
TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
        0.20        84.72        62.79        39.58         6.67 

$`AMP PEAK 20(17Q25.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57        71.80       133.25        28.08        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH 
      103.10        65.49        23.77       115.53       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 
       12.10        56.19        66.08        45.11        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
      166.52        60.23        13.87       103.59        39.75       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
       43.69        40.14       131.90        18.38        51.68       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JX 
      135.75       137.92       166.19       125.19        54.67         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       11.34         3.25        25.18        66.25        22.95        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB 
       20.38       176.55        35.93       107.34        53.92        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       28.60        15.68        13.87        17.85        45.11        35.01 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       52.01         6.35        12.20        29.82         8.65        94.98 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       26.89       109.64       151.27        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S 
       47.84        39.62        72.07        44.35        37.35        55.92 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
      345.96       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       39.29       314.56       135.95        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97       101.95        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ 
      129.27        19.76        61.51       103.27       103.20        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA 
      144.76       203.05       167.90        43.23        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73         3.68        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 
      127.20        64.08        34.32        27.35        33.40        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF 
       61.05       162.08        37.25        79.99        23.34        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       31.27        32.05       247.04       174.21         4.90       210.08 
TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       15.16       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW 
       32.75        47.38        74.73        11.41       148.80        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
      174.84        12.43        26.73        49.45        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
      117.93        10.13        64.44        32.48        46.36        12.62 
TCGA-OD-A75X 
      294.77 

  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                          0.20                           0.16 
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                        248.65                         357.37 
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                         48.59                          47.54 
[1] "0.2 - 248.7 (48.6)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1"  
D20V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 20(17Q25.3) MUTATED                   14             1
  AMP PEAK 20(17Q25.3) WILD-TYPE                 23             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 20(17Q25.3) MUTATED                                          16
  AMP PEAK 20(17Q25.3) WILD-TYPE                                        44
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 20(17Q25.3) MUTATED                    65
  AMP PEAK 20(17Q25.3) WILD-TYPE                 114
D20V4, multiclass
                                           clus
vv                                          AMP PEAK 20(17Q25.3) MUTATED
  DISTANT METASTASIS                                                  14
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           16
  REGIONAL LYMPH NODE                                                 65
                                           clus
vv                                          AMP PEAK 20(17Q25.3) WILD-TYPE
  DISTANT METASTASIS                                                    23
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             44
  REGIONAL LYMPH NODE                                                  114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 20(17Q25.3) MUTATED             4       2       9        5        9
  AMP PEAK 20(17Q25.3) WILD-TYPE           6       4      14        5       16
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 20(17Q25.3) MUTATED          6         1         4         6
  AMP PEAK 20(17Q25.3) WILD-TYPE       11         9        10         4
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 20(17Q25.3) MUTATED           9          2         11         17
  AMP PEAK 20(17Q25.3) WILD-TYPE        23         12         12         31
                                vv
clus                             STAGE IV
  AMP PEAK 20(17Q25.3) MUTATED          4
  AMP PEAK 20(17Q25.3) WILD-TYPE        8
D20V5, multiclass
             clus
vv            AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE
  I OR II NOS                            4                              6
  STAGE 0                                2                              4
  STAGE I                                9                             14
  STAGE IA                               5                              5
  STAGE IB                               9                             16
  STAGE II                               6                             11
  STAGE IIA                              1                              9
  STAGE IIB                              4                             10
  STAGE IIC                              6                              4
  STAGE III                              9                             23
  STAGE IIIA                             2                             12
  STAGE IIIB                            11                             12
  STAGE IIIC                            17                             31
  STAGE IV                               4                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 20(17Q25.3) MUTATED      19 25 14 23
  AMP PEAK 20(17Q25.3) WILD-TYPE    34 35 41 34
D20V6, multiclass
       clus
vv      AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE
  T0+T1                           19                             34
  T2                              25                             35
  T3                              14                             41
  T4                              23                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 20(17Q25.3) MUTATED   51 17 12 12
  AMP PEAK 20(17Q25.3) WILD-TYPE 90 34 20 25
D20V7, multiclass
    clus
vv   AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE
  N0                           51                             90
  N1                           17                             34
  N2                           12                             20
  N3                           12                             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 20(17Q25.3) MUTATED    87   1   1   1   2
  AMP PEAK 20(17Q25.3) WILD-TYPE 165   3   1   1   3
D20V8, multiclass
     clus
vv    AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE
  M0                            87                            165
  M1                             1                              3
  M1A                            1                              1
  M1B                            1                              1
  M1C                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                                cls
clus                              0  1
  AMP PEAK 20(17Q25.3) MUTATED   32 27
  AMP PEAK 20(17Q25.3) WILD-TYPE 72 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.3) MUTATED     32   27
  AMP PEAK 20(17Q25.3) WILD-TYPE   72   45
     clus
vv    AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE
  NO                            32                             72
  YES                           27                             45
[1] 2 2
[1] FALSE
D20V10, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q25.3) MUTATED    11  85
  AMP PEAK 20(17Q25.3) WILD-TYPE  23 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.3) MUTATED     11   85
  AMP PEAK 20(17Q25.3) WILD-TYPE   23  162
     clus
vv    AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE
  NO                            11                             23
  YES                           85                            162
[1] 2 2
[1] FALSE
D20V11, continuous
D20V12, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q25.3) MUTATED    33  63
  AMP PEAK 20(17Q25.3) WILD-TYPE  75 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.3) MUTATED     33   63
  AMP PEAK 20(17Q25.3) WILD-TYPE   75  110
        clus
vv       AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE
  FEMALE                           33                             75
  MALE                             63                            110
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(17Q25.3) MUTATED       2                         1    93
  AMP PEAK 20(17Q25.3) WILD-TYPE     3                         0   182
D20V13, multiclass
                           clus
vv                          AMP PEAK 20(17Q25.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               93
                           clus
vv                          AMP PEAK 20(17Q25.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q25.3) MUTATED     1  94
  AMP PEAK 20(17Q25.3) WILD-TYPE   2 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.3) MUTATED      1   94
  AMP PEAK 20(17Q25.3) WILD-TYPE    2  180
                        clus
vv                       AMP PEAK 20(17Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       AMP PEAK 20(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            180
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(19P13.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(19P13.2) MUTATED    27  26
  AMP PEAK 21(19P13.2) WILD-TYPE 110 107
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            53                            217 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            26                            107 
$`AMP PEAK 21(19P13.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       32.42        70.16        81.24        88.50        69.90        30.87 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A5GU TCGA-D9-A6E9 
       64.44        45.11        26.37        20.48        23.11         9.90 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A180 
       13.22        10.03         6.64        17.56        10.55         8.12 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2GH TCGA-EE-A2GO 
       38.63         1.08        12.03         8.84        47.21        30.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A3J4 
       98.27         2.70        44.25        56.02        29.65        22.92 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19J TCGA-ER-A2ND TCGA-ER-A3ET 
       33.60         5.72        11.90         4.21         1.87         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
        1.71        18.41         6.71         3.45        11.01        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS 
        7.33        20.38         8.22        12.92        47.38        49.15 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GN-A266 TCGA-GN-A267 
        3.22        28.73         0.20        10.13        16.24 

$`AMP PEAK 21(19P13.2) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47         8.52       111.09       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       45.83        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.41         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       13.32        24.00         6.31         9.34       103.59         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       13.94        95.38        52.01        47.87         1.55         6.97 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01         2.89        11.31        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       25.15         4.93        22.36        19.36         7.00        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       13.15         0.20         0.13         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.20        11.57         6.31         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
        4.41        27.12         9.50         8.09         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        47.51         9.53        29.46         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       63.42       111.78       111.91        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       13.94        31.40        18.61        12.95        38.40        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       25.18         3.78         3.52        11.11       114.15        34.88 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        78.44        11.80         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       11.74         9.04        22.49        85.74         4.90         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        5.36        64.47        23.80        15.52         7.30         3.39 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP 
       19.53        11.08         7.17        30.87        12.89        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23        53.85         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       15.42        12.16        14.70        11.84        10.65        11.05 
TCGA-QB-A6FS 
        5.79 

  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           0.2                            0.0 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                         98.27                         124.31 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                         16.24                          13.94 
[1] "0.2 - 98.3 (16.2)"  "0.0 - 124.3 (13.9)"
[1] "hr=" "1"  
D21V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(19P13.2) MUTATED    27  26
  AMP PEAK 21(19P13.2) WILD-TYPE 115 108
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            53                            223 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            26                            108 
$`AMP PEAK 21(19P13.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
      112.57        71.80        95.74       115.53        69.90        48.76 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A5GU TCGA-D9-A6E9 
       66.08        45.11        39.75        51.68       125.19         9.90 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A180 
       66.25        20.38        68.09       215.44        27.22        94.98 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2GH TCGA-EE-A2GO 
       39.62         2.60        56.42        14.47       208.04       101.95 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A3J4 
      129.27        28.83       103.20       167.90       103.56       127.20 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19J TCGA-ER-A2ND TCGA-ER-A3ET 
      148.08         9.17        13.02         6.44        23.34        80.32 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       33.21        92.98       210.08        48.59       228.59        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS 
        7.79       357.37        53.52        47.38       101.26       148.80 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GN-A266 TCGA-GN-A267 
       50.14        28.73         0.20        10.13        64.44 

$`AMP PEAK 21(19P13.2) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57        16.67       112.04       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       60.23        24.53        13.87         9.34       103.59        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       15.06       110.93       135.75       137.92       166.19         7.43 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       25.18        22.95        48.89        36.03       117.21       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       23.44        28.60        10.49        15.68        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       17.85        45.11        35.01         3.55        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       12.20        29.82         8.65        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        80.61        47.84        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       32.19        44.35        18.61        37.35        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        61.51        47.28       103.27        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       144.76       203.05        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
      101.79        31.40        35.44        13.94        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        12.59        26.37       268.93       152.35 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        43.82        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       32.05       247.04        46.98       174.21         4.90        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        7.00       216.92       202.65        28.08        27.72        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP 
       40.27        15.45         9.70        32.75        23.93        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55        11.41        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        66.67       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88        22.92        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       62.79        32.48        39.58        46.36        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                          0.20                           0.16 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                        357.37                         345.96 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                         64.44                          46.82 
[1] "0.2 - 357.4 (64.4)" "0.2 - 346.0 (46.8)"
[1] "hr=" "1.2"
D21V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 21(19P13.2) MUTATED                    7             2
  AMP PEAK 21(19P13.2) WILD-TYPE                 30             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 21(19P13.2) MUTATED                                          15
  AMP PEAK 21(19P13.2) WILD-TYPE                                        45
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 21(19P13.2) MUTATED                    29
  AMP PEAK 21(19P13.2) WILD-TYPE                 150
D21V4, multiclass
                                           clus
vv                                          AMP PEAK 21(19P13.2) MUTATED
  DISTANT METASTASIS                                                   7
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           15
  REGIONAL LYMPH NODE                                                 29
                                           clus
vv                                          AMP PEAK 21(19P13.2) WILD-TYPE
  DISTANT METASTASIS                                                    30
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             45
  REGIONAL LYMPH NODE                                                  150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 21(19P13.2) MUTATED             2       0       9        1        4
  AMP PEAK 21(19P13.2) WILD-TYPE           8       6      14        9       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 21(19P13.2) MUTATED          4         3         0         2
  AMP PEAK 21(19P13.2) WILD-TYPE       13         7        14         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 21(19P13.2) MUTATED           5          6          3          8
  AMP PEAK 21(19P13.2) WILD-TYPE        27          8         20         40
                                vv
clus                             STAGE IV
  AMP PEAK 21(19P13.2) MUTATED          5
  AMP PEAK 21(19P13.2) WILD-TYPE        7
D21V5, multiclass
             clus
vv            AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  I OR II NOS                            2                              8
  STAGE 0                                0                              6
  STAGE I                                9                             14
  STAGE IA                               1                              9
  STAGE IB                               4                             21
  STAGE II                               4                             13
  STAGE IIA                              3                              7
  STAGE IIB                              0                             14
  STAGE IIC                              2                              8
  STAGE III                              5                             27
  STAGE IIIA                             6                              8
  STAGE IIIB                             3                             20
  STAGE IIIC                             8                             40
  STAGE IV                               5                              7
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 21(19P13.2) MUTATED       9 14 14 10
  AMP PEAK 21(19P13.2) WILD-TYPE    44 46 41 47
D21V6, multiclass
       clus
vv      AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  T0+T1                            9                             44
  T2                              14                             46
  T3                              14                             41
  T4                              10                             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 21(19P13.2) MUTATED    29  10   5   8
  AMP PEAK 21(19P13.2) WILD-TYPE 112  41  27  29
D21V7, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  N0                           29                            112
  N1                           10                             41
  N2                            5                             27
  N3                            8                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 21(19P13.2) MUTATED    47   3   2   0   0
  AMP PEAK 21(19P13.2) WILD-TYPE 205   1   0   2   5
D21V8, multiclass
     clus
vv    AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  M0                            47                            205
  M1                             3                              1
  M1A                            2                              0
  M1B                            0                              2
  M1C                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                                cls
clus                              0  1
  AMP PEAK 21(19P13.2) MUTATED   23 12
  AMP PEAK 21(19P13.2) WILD-TYPE 81 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     23   12
  AMP PEAK 21(19P13.2) WILD-TYPE   81   60
     clus
vv    AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  NO                            23                             81
  YES                           12                             60
[1] 2 2
[1] FALSE
D21V10, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED     7  46
  AMP PEAK 21(19P13.2) WILD-TYPE  27 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED      7   46
  AMP PEAK 21(19P13.2) WILD-TYPE   27  201
     clus
vv    AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  NO                             7                             27
  YES                           46                            201
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    21  32
  AMP PEAK 21(19P13.2) WILD-TYPE  87 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     21   32
  AMP PEAK 21(19P13.2) WILD-TYPE   87  141
        clus
vv       AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  FEMALE                           21                             87
  MALE                             32                            141
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(19P13.2) MUTATED       1                         0    52
  AMP PEAK 21(19P13.2) WILD-TYPE     4                         1   223
D21V13, multiclass
                           clus
vv                          AMP PEAK 21(19P13.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               52
                           clus
vv                          AMP PEAK 21(19P13.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED     0  52
  AMP PEAK 21(19P13.2) WILD-TYPE   3 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED      0   52
  AMP PEAK 21(19P13.2) WILD-TYPE    3  222
                        clus
vv                       AMP PEAK 21(19P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       AMP PEAK 21(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            222
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(20Q13.33) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 22(20Q13.33) MUTATED   73 67
  AMP PEAK 22(20Q13.33) WILD-TYPE 64 66
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                            140                             130 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             67                              66 
$`AMP PEAK 22(20Q13.33) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       16.47        32.42        22.55        21.14        88.50        69.90 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       11.41        30.87         7.50        36.16        92.42        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
       45.11        15.25        82.29        61.38        13.32       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       26.37         5.39        41.10        17.72        20.48        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       47.87         1.55        23.11         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA 
       13.22        35.80        10.03        13.68        36.69         4.93 
TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A183 
       17.56         0.00         0.20        10.55         8.12        12.20 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E 
        5.13        36.07         9.21         7.99        11.15        38.63 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
        1.08        12.03         8.84         6.48         8.68         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       49.22         9.67         8.94        39.39        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
       30.08        28.31        33.83        30.84         5.42        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG 
        8.84        98.27         2.70         6.18        47.51        44.25 
TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
        7.96        26.99        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 
      122.73        25.84         3.68        30.15        15.95         3.22 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       21.60        21.60        22.22        13.94        33.60        31.40 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19J 
       12.95         5.72        25.18        11.90       114.15         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
       13.45        28.60        34.68        17.72        11.80         1.87 
TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       12.62         1.71        18.41        85.74         4.90         6.71 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
        3.45        23.80        15.52         7.33         7.30        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
        8.22        19.53         7.17        12.92        12.89        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 
        8.65        49.15        40.64         8.68         0.82         3.22 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GN-A264 
       28.73        14.20         2.27         0.20         7.23        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       84.72        16.24        15.42        12.16        14.70        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

$`AMP PEAK 22(20Q13.33) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        70.16       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JK 
       81.24        10.29        85.32         8.38        68.22         6.31 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A3ML 
       64.44       114.67        46.98        46.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T 
        9.34        80.22        42.71        15.09         8.84        13.94 
TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       95.38         6.97         4.01        14.60        48.79        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       39.19         9.99        44.52        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       19.36         7.00        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.00        13.22        11.57         6.31         1.12         1.35 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
        4.31         4.34         5.13         1.18         9.90        37.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S 
        8.55         4.41        27.12         9.50         8.09         9.99 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ 
        2.43        11.31        23.90        34.29        17.98        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MD 
       16.01        35.54         1.15        13.02        34.98         9.53 
TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       29.46        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
       25.08        21.60        29.65        13.81        12.72        22.92 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       16.14        27.35         0.46        18.61        38.40        76.41 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19Q 
        3.78         3.52        11.11        34.88        42.84         9.57 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       36.07        78.44         1.51        13.08        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY 
        6.58        22.49         3.58         5.36        64.47        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR 
       14.24         3.39        11.08        30.87        52.08         8.81 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.39         5.23        53.85         7.36        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 
       12.85        24.85        10.13        11.84 

  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                              0                               0 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                         124.31                          114.67 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                         15.335                          13.185 
[1] "0.0 - 124.3 (15.3)" "0.0 - 114.7 (13.2)"
[1] "hr=" "1.1"
D22V2, survival
                                 sevent
clus2                              0  1
  AMP PEAK 22(20Q13.33) MUTATED   75 68
  AMP PEAK 22(20Q13.33) WILD-TYPE 67 66
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                            143                             133 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             68                              66 
$`AMP PEAK 22(20Q13.33) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       16.57       112.57        31.59        23.77       115.53        69.90 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87        48.76       113.52        42.08       171.58        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
       45.11        58.06       166.52        86.93        60.23       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       39.75        21.47       131.90        18.38        51.68       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z3 
      137.92       166.19       125.19       151.53         6.41         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.90        25.18        66.25        36.03        20.38       176.55 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 
       61.18        65.92       215.44        35.01         3.55        12.20 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H 
       27.22        94.98        26.89        68.15       109.64       168.26 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       63.35        13.97        39.62         2.60        56.42        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      345.96       171.55        17.92       102.90        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN 
       47.54       135.95       208.04        48.72        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      101.95        13.91        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MS 
       19.76        61.51       103.20        16.96       248.65       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
       54.51        23.47       172.18        36.95        64.08        53.19 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      101.79       148.08        31.40        13.94         9.17        98.40 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       13.02       268.93         6.44       131.51        61.05       162.08 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A3YN 
      148.18        43.82        23.34        31.27        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 
      174.21         4.90       210.08        48.59       202.65        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        27.72       357.37        53.52        40.27         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        23.93       101.26       133.55       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD 
       26.56        27.09        50.14        28.73       174.84        77.88 
TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        0.20         7.23       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        39.58        12.62       294.77         6.67 

$`AMP PEAK 22(20Q13.33) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JK 
       95.74        43.43       103.10        65.49       168.00        12.10 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A3ML 
       66.08       130.72        46.98        46.32        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T 
        9.34       161.85        43.69        40.14        10.03        15.06 
TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A6EG 
      110.93         7.43        54.67         3.65        11.34        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       48.89       117.21       194.83        35.93       107.34        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       10.16        17.85        45.11        52.01         6.35        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        8.65        33.73        14.70         4.96       151.27        78.87 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       13.55        80.61        47.84        72.07        32.19        44.35 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 
       18.61        37.35        55.92        25.87        46.82        24.43 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR 
       67.43       314.56        89.33        54.74        79.66        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ 
       55.59        44.88        47.28       103.27       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      144.76       203.05       167.90        47.54        43.23       103.56 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       13.81       138.81       127.20        34.32        27.35        33.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       35.44        50.76        77.75        48.89        12.59        26.37 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE 
      152.35        44.05        50.89        37.25        79.99        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 
       16.37        32.05       247.04        80.32        46.98        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZF 
        7.00       216.92       228.59        20.91        48.85        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
       32.75        74.73        11.41        49.48        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
       66.67        12.43        26.73        49.45        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
        0.16         2.40         9.90        14.04       120.46        10.13 
TCGA-GN-A4U8 
       46.36 

  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                           0.20                            0.16 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                         357.37                          314.56 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                          53.52                           45.11 
[1] "0.2 - 357.4 (53.5)" "0.2 - 314.6 (45.1)"
[1] "hr=" "1.3"
D22V3, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 22(20Q13.33) MUTATED                   21             3
  AMP PEAK 22(20Q13.33) WILD-TYPE                 16             1
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 22(20Q13.33) MUTATED                                          29
  AMP PEAK 22(20Q13.33) WILD-TYPE                                        31
                                 vv
clus                              REGIONAL LYMPH NODE
  AMP PEAK 22(20Q13.33) MUTATED                    93
  AMP PEAK 22(20Q13.33) WILD-TYPE                  86
D22V4, multiclass
                                           clus
vv                                          AMP PEAK 22(20Q13.33) MUTATED
  DISTANT METASTASIS                                                   21
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            29
  REGIONAL LYMPH NODE                                                  93
                                           clus
vv                                          AMP PEAK 22(20Q13.33) WILD-TYPE
  DISTANT METASTASIS                                                     16
  PRIMARY TUMOR                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                              31
  REGIONAL LYMPH NODE                                                    86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 22(20Q13.33) MUTATED             8       3      16        7       16
  AMP PEAK 22(20Q13.33) WILD-TYPE           2       3       7        3        9
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 22(20Q13.33) MUTATED          8         3         3         7
  AMP PEAK 22(20Q13.33) WILD-TYPE        9         7        11         3
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 22(20Q13.33) MUTATED          19          8         13         20
  AMP PEAK 22(20Q13.33) WILD-TYPE        13          6         10         28
                                 vv
clus                              STAGE IV
  AMP PEAK 22(20Q13.33) MUTATED          4
  AMP PEAK 22(20Q13.33) WILD-TYPE        8
D22V5, multiclass
             clus
vv            AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  I OR II NOS                             8                               2
  STAGE 0                                 3                               3
  STAGE I                                16                               7
  STAGE IA                                7                               3
  STAGE IB                               16                               9
  STAGE II                                8                               9
  STAGE IIA                               3                               7
  STAGE IIB                               3                              11
  STAGE IIC                               7                               3
  STAGE III                              19                              13
  STAGE IIIA                              8                               6
  STAGE IIIB                             13                              10
  STAGE IIIC                             20                              28
  STAGE IV                                4                               8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  AMP PEAK 22(20Q13.33) MUTATED      32 38 22 29
  AMP PEAK 22(20Q13.33) WILD-TYPE    21 22 33 28
D22V6, multiclass
       clus
vv      AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  T0+T1                            32                              21
  T2                               38                              22
  T3                               22                              33
  T4                               29                              28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  AMP PEAK 22(20Q13.33) MUTATED   79 30 13 17
  AMP PEAK 22(20Q13.33) WILD-TYPE 62 21 19 20
D22V7, multiclass
    clus
vv   AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  N0                            79                              62
  N1                            30                              21
  N2                            13                              19
  N3                            17                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B M1C
  AMP PEAK 22(20Q13.33) MUTATED   135   2   2   1   0
  AMP PEAK 22(20Q13.33) WILD-TYPE 117   2   0   1   5
D22V8, multiclass
     clus
vv    AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  M0                            135                             117
  M1                              2                               2
  M1A                             2                               0
  M1B                             1                               1
  M1C                             0                               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q13.33) MUTATED   60 33
  AMP PEAK 22(20Q13.33) WILD-TYPE 44 39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.33) MUTATED     60   33
  AMP PEAK 22(20Q13.33) WILD-TYPE   44   39
     clus
vv    AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  NO                             60                              44
  YES                            33                              39
[1] 2 2
[1] FALSE
D22V10, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.33) MUTATED    18 129
  AMP PEAK 22(20Q13.33) WILD-TYPE  16 118
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.33) MUTATED     18  129
  AMP PEAK 22(20Q13.33) WILD-TYPE   16  118
     clus
vv    AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  NO                             18                              16
  YES                           129                             118
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q13.33) MUTATED   55 92
  AMP PEAK 22(20Q13.33) WILD-TYPE 53 81
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.33) MUTATED     55   92
  AMP PEAK 22(20Q13.33) WILD-TYPE   53   81
        clus
vv       AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  FEMALE                            55                              53
  MALE                              92                              81
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(20Q13.33) MUTATED       2                         0   145
  AMP PEAK 22(20Q13.33) WILD-TYPE     3                         1   130
D22V13, multiclass
                           clus
vv                          AMP PEAK 22(20Q13.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               145
                           clus
vv                          AMP PEAK 22(20Q13.33) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                 130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.33) MUTATED     1 144
  AMP PEAK 22(20Q13.33) WILD-TYPE   2 130
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.33) MUTATED      1  144
  AMP PEAK 22(20Q13.33) WILD-TYPE    2  130
                        clus
vv                       AMP PEAK 22(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           144
                        clus
vv                       AMP PEAK 22(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             130
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(22Q13.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 23(22Q13.2) MUTATED   63 54
  AMP PEAK 23(22Q13.2) WILD-TYPE 74 79
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                           117                            153 
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                            54                             79 
$`AMP PEAK 23(22Q13.2) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       16.47        22.55        85.32        88.50        68.22        69.90 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
       92.42        64.44        45.11        15.25        61.38        13.32 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
        9.34        26.37         5.39        13.94        95.38        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        1.55         6.97         4.01         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 
       48.79        35.80        51.12        10.03        39.19        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SG 
       25.15         4.93        22.36        17.56         0.13         0.00 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 
        0.00         0.20        10.55         6.31         8.12         5.13 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
        9.21         1.08        27.12         9.50         8.09         8.84 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.68         8.09        23.90         9.67         8.94        39.39 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2M6 
       47.21        30.08        28.31        33.83        30.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
        2.70        29.46        63.42        25.08        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       27.16         5.56       124.31       122.73         3.68        30.15 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C 
       15.95        21.60        21.60        27.35        25.18         3.78 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A2NG 
      114.15        13.45        28.60        17.72        13.08        12.62 
TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YY 
        6.58        18.41        85.74         4.90         6.71        11.01 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.33         7.30         8.22        19.53         7.17        30.87 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       12.89        47.38         8.65        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD 
       27.39         0.82         3.22         7.36        28.73         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        0.20         0.13        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

$`AMP PEAK 23(22Q13.2) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       45.83        81.24        10.29         8.38        21.14        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ 
       30.87         7.50        36.16         6.31        56.19       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR 
       46.98        46.32        82.29        24.00         6.31       103.59 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1I2 
       20.48        47.87        23.11         2.89        14.60        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        9.99        44.52         6.64        19.36         7.00        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       13.15         0.20        13.22        11.57         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       12.20         4.31        36.07         4.34         5.13         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
        4.41        12.03         9.99         6.48         2.43        11.31 
TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       49.22        34.29        17.98        34.92        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       35.54         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH 
        8.84         6.18        47.51         9.53        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT 
       14.56       111.78       111.91        56.02        26.99        23.05 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       25.84        13.81        12.72         3.22        22.92        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E 
       12.95        38.40         5.72        76.41         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       11.11        34.88         4.21        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH 
       36.07        78.44        11.80         1.87         1.51        11.74 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
        9.04        22.49         1.71         3.58         5.36        64.47 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC 
        3.45        23.80        14.24        15.52         3.39        20.38 
TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZZ TCGA-FS-A4F0 
       11.08        12.92        52.08         8.81         5.23        53.85 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV 
       14.20        10.78         5.98         6.41         0.99         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
        0.43         9.90         7.23        12.85        24.85        10.13 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       11.84        10.65        11.05 

  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                          0.00                           0.16 
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                        124.31                         114.67 
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                         15.95                          13.22 
[1] "0.0 - 124.3 (15.9)" "0.2 - 114.7 (13.2)"
[1] "hr=" "1.2"
D23V2, survival
                                sevent
clus2                             0  1
  AMP PEAK 23(22Q13.2) MUTATED   65 55
  AMP PEAK 23(22Q13.2) WILD-TYPE 77 79
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                           120                            156 
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                            55                             79 
$`AMP PEAK 23(22Q13.2) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       16.57        31.59       103.10       115.53       168.00        69.90 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
      171.58        66.08        45.11        58.06        86.93        60.23 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
        9.34        39.75        21.47        15.06       110.93       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 
      166.19         7.43       151.53         6.41        11.34         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        66.25        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 
      194.83        61.18        53.92        65.92        23.44       215.44 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y 
       17.85        45.11        35.01         3.55        12.20        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A29M 
        8.65        94.98        68.15       168.26         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 
       18.61        37.35        14.47       171.55        17.92        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
       39.29        58.75        47.54       208.04        48.72        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MJ 
       90.97       101.95       129.27        28.83       103.27        96.23 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54        43.23       103.56       136.47        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 
      122.73         3.68        54.51        23.47        36.95        64.08 
TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
       27.35        98.40        48.89       268.93       131.51        61.05 
TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A 
      148.18        16.37        31.27        80.32        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD 
        4.90       210.08       228.59         7.79        27.72        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       40.27         9.70        32.75        23.93       101.26       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 
      148.80        53.16        26.56        49.48        27.09        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 
       66.67        28.73        77.88         0.20        47.54       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       84.72        64.44        62.79        32.48        39.58         6.67 

$`AMP PEAK 23(22Q13.2) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       90.90        95.74        43.43        65.49        23.77        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ 
       48.76       113.52        42.08        12.10        56.19       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR 
       46.98        46.32       166.52        24.53        13.87       103.59 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 
       51.68       137.92       125.19        54.67         3.65         3.25 
TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 
       22.95       176.55        35.93       107.34        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV 
       10.49        15.68        13.87        10.16        52.01         6.35 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       29.82        33.73        14.70        26.89         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        78.87        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S 
       13.97        39.62        72.07        32.19        56.42        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD 
      345.96        25.87        46.82       102.90        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR 
      135.95        89.33        54.74        79.66        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       55.59        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       47.28       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH 
      167.90       248.65        41.59        25.84        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
      172.18       127.20        34.32        53.19        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       77.75        12.59        13.02        26.37       152.35         6.44 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
       44.05       162.08        50.89        37.25        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       23.34        20.15        32.05       247.04        46.98        33.21 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.16         7.00       216.92        48.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       28.08        48.85       357.37        15.45        47.38        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       11.41        27.02        77.82       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       49.45        22.92         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       14.04       120.46        10.13        46.36        12.62       294.77 

  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                          0.20                           0.16 
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                        268.93                         357.37 
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                         51.65                          46.59 
[1] "0.2 - 268.9 (51.6)" "0.2 - 357.4 (46.6)"
[1] "hr=" "1.1"
D23V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 23(22Q13.2) MUTATED                   15             4
  AMP PEAK 23(22Q13.2) WILD-TYPE                 22             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 23(22Q13.2) MUTATED                                          28
  AMP PEAK 23(22Q13.2) WILD-TYPE                                        32
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 23(22Q13.2) MUTATED                    75
  AMP PEAK 23(22Q13.2) WILD-TYPE                 104
D23V4, multiclass
                                           clus
vv                                          AMP PEAK 23(22Q13.2) MUTATED
  DISTANT METASTASIS                                                  15
  PRIMARY TUMOR                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           28
  REGIONAL LYMPH NODE                                                 75
                                           clus
vv                                          AMP PEAK 23(22Q13.2) WILD-TYPE
  DISTANT METASTASIS                                                    22
  PRIMARY TUMOR                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             32
  REGIONAL LYMPH NODE                                                  104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  AMP PEAK 23(22Q13.2) MUTATED             4       3      10        4        9
  AMP PEAK 23(22Q13.2) WILD-TYPE           6       3      13        6       16
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 23(22Q13.2) MUTATED          6         4         4         6
  AMP PEAK 23(22Q13.2) WILD-TYPE       11         6        10         4
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 23(22Q13.2) MUTATED          17          8         10         23
  AMP PEAK 23(22Q13.2) WILD-TYPE        15          6         13         25
                                vv
clus                             STAGE IV
  AMP PEAK 23(22Q13.2) MUTATED          4
  AMP PEAK 23(22Q13.2) WILD-TYPE        8
D23V5, multiclass
             clus
vv            AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE
  I OR II NOS                            4                              6
  STAGE 0                                3                              3
  STAGE I                               10                             13
  STAGE IA                               4                              6
  STAGE IB                               9                             16
  STAGE II                               6                             11
  STAGE IIA                              4                              6
  STAGE IIB                              4                             10
  STAGE IIC                              6                              4
  STAGE III                             17                             15
  STAGE IIIA                             8                              6
  STAGE IIIB                            10                             13
  STAGE IIIC                            23                             25
  STAGE IV                               4                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 23(22Q13.2) MUTATED      24 32 18 26
  AMP PEAK 23(22Q13.2) WILD-TYPE    29 28 37 31
D23V6, multiclass
       clus
vv      AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE
  T0+T1                           24                             29
  T2                              32                             28
  T3                              18                             37
  T4                              26                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 23(22Q13.2) MUTATED   55 25 16 18
  AMP PEAK 23(22Q13.2) WILD-TYPE 86 26 16 19
D23V7, multiclass
    clus
vv   AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE
  N0                           55                             86
  N1                           25                             26
  N2                           16                             16
  N3                           18                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  AMP PEAK 23(22Q13.2) MUTATED   109   1   1   1   2
  AMP PEAK 23(22Q13.2) WILD-TYPE 143   3   1   1   3
D23V8, multiclass
     clus
vv    AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE
  M0                           109                            143
  M1                             1                              3
  M1A                            1                              1
  M1B                            1                              1
  M1C                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                                cls
clus                              0  1
  AMP PEAK 23(22Q13.2) MUTATED   46 35
  AMP PEAK 23(22Q13.2) WILD-TYPE 58 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(22Q13.2) MUTATED     46   35
  AMP PEAK 23(22Q13.2) WILD-TYPE   58   37
     clus
vv    AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE
  NO                            46                             58
  YES                           35                             37
[1] 2 2
[1] FALSE
D23V10, binary
                                cls
clus                               0   1
  AMP PEAK 23(22Q13.2) MUTATED    15 107
  AMP PEAK 23(22Q13.2) WILD-TYPE  19 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(22Q13.2) MUTATED     15  107
  AMP PEAK 23(22Q13.2) WILD-TYPE   19  140
     clus
vv    AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE
  NO                            15                             19
  YES                          107                            140
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, binary
                                cls
clus                               0   1
  AMP PEAK 23(22Q13.2) MUTATED    50  72
  AMP PEAK 23(22Q13.2) WILD-TYPE  58 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(22Q13.2) MUTATED     50   72
  AMP PEAK 23(22Q13.2) WILD-TYPE   58  101
        clus
vv       AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE
  FEMALE                           50                             58
  MALE                             72                            101
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(22Q13.2) MUTATED       3                         1   118
  AMP PEAK 23(22Q13.2) WILD-TYPE     2                         0   157
D23V13, multiclass
                           clus
vv                          AMP PEAK 23(22Q13.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              118
                           clus
vv                          AMP PEAK 23(22Q13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                                cls
clus                               0   1
  AMP PEAK 23(22Q13.2) MUTATED     0 120
  AMP PEAK 23(22Q13.2) WILD-TYPE   3 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(22Q13.2) MUTATED      0  120
  AMP PEAK 23(22Q13.2) WILD-TYPE    3  154
                        clus
vv                       AMP PEAK 23(22Q13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       AMP PEAK 23(22Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            154
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    35  31
  DEL PEAK  1(1P36.31) WILD-TYPE 102 102
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            66                            204 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            31                            102 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE 
       16.47       111.09         6.31        64.44        15.25        13.32 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-DA-A1I0 TCGA-DA-A1I2 
        5.39        52.01         1.55         6.97        10.03        13.68 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 
       36.69        17.56        14.83         0.00        10.55         8.12 
TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29R 
        1.35         5.13         9.21         9.90        11.15         8.84 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M5 
       34.92        47.21        30.08        30.84         1.15         8.84 
TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AD 
        9.53         7.96       111.78        27.16       122.73         3.68 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       13.81         3.22        22.22         3.78         3.52       114.15 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL 
       36.07         1.87         1.51        11.74        22.49         1.71 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.90         3.58        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z7 TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 
        7.33        12.92        40.64        27.39         0.82        14.20 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A26D 
        6.41         2.27         0.20         0.13         0.16        14.70 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
        8.52        32.42        70.16       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       36.16        92.42        56.19        45.11       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        61.38        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        26.37        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        95.38        47.87 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       14.60        48.79        35.80        51.12        39.19         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN 
        7.00        13.15         0.20         0.13         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
        0.20        11.57         6.31         1.12        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C 
        4.31        36.07         4.34         1.18         7.99        37.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       12.03         8.09         9.99         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       39.39        34.29        17.98        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       28.31        33.83         5.42        13.02        34.98        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       98.27         2.70         6.18        47.51        29.46        44.25 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       14.56        63.42       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       21.60        29.65        23.05         5.56       124.31        25.84 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       30.15        15.95        12.72        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90        11.11        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84        34.68         9.57        17.72        78.44        11.80 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A 
       13.08        12.62         9.04         6.58        18.41        85.74 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        6.71         5.36        14.24        15.52         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.68         5.23        53.85         3.22         7.36        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       10.78         5.98         0.99         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       15.42        12.16        11.84        10.65        11.05         5.79 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             0                              0 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        10.290                         16.075 
[1] "0.0 - 122.7 (10.3)" "0.0 - 124.3 (16.1)"
[1] "hr=" "1.3"
D24V2, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    35  32
  DEL PEAK  1(1P36.31) WILD-TYPE 107 102
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            67                            209 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            32                            102 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE 
       16.57       112.04        12.10        66.08        58.06        60.23 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1JX TCGA-DA-A1I0 
       21.47       135.75       166.19         7.43         6.41        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EE-A17Y 
      176.55        61.18       215.44        15.68        35.01        27.22 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D 
       94.98        14.70        78.87       168.26        80.61        13.97 
TCGA-EE-A29R TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2GR 
       14.47       135.95       208.04        48.72       101.95        14.30 
TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AB 
       21.67        47.28        16.96       144.76       136.47       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A19C TCGA-ER-A19D 
        3.68        13.81       172.18        53.19        48.89        12.59 
TCGA-ER-A19G TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3EV 
      268.93        37.25        23.34        20.15        32.05        46.98 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       33.21         4.90        15.16       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
      202.65         7.79        47.38        53.16        49.48        27.09 
TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
      174.84        49.45        77.88         0.20        47.54         0.16 
TCGA-GN-A26D 
       39.58 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       42.08       171.58        56.19        45.11       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       110.93       137.92 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19       151.53        54.67         3.65        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
      117.21       194.83        35.93       107.34        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R 
       23.44        68.09        28.60        10.49        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       17.85        45.11         3.55        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       29.82         8.65        33.73        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
      109.64       151.27        13.55        63.35        47.84        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        55.92       345.96        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       67.43       314.56        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       90.97        13.91        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
       28.83        19.76        61.51       103.27       103.20       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
      103.56        41.59        53.26       124.31        25.84        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E 
       13.94        50.76         9.17        77.75        98.40        13.02 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
      162.08        50.89       148.18        79.99        43.82        16.37 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
       31.27       247.04        80.32        92.98       174.21       210.08 
TCGA-FR-A7U9 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
        7.00        20.91        28.08        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
       53.52        40.27        15.45         9.70        32.75        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
      101.26        74.73       133.55        11.41       148.80        26.56 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67        28.73        12.43 
TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       26.73        22.92         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        46.36        12.62       294.77         6.67 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.16                           2.40 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        268.93                         357.37 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         47.54                          47.84 
[1] "0.2 - 268.9 (47.5)" "2.4 - 357.4 (47.8)"
[1] "hr=" "1.1"
D24V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  1(1P36.31) MUTATED                   15             0
  DEL PEAK  1(1P36.31) WILD-TYPE                 22             4
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  1(1P36.31) MUTATED                                          12
  DEL PEAK  1(1P36.31) WILD-TYPE                                        48
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK  1(1P36.31) MUTATED                    41
  DEL PEAK  1(1P36.31) WILD-TYPE                 138
D24V4, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.31) MUTATED
  DISTANT METASTASIS                                                  15
  PRIMARY TUMOR                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           12
  REGIONAL LYMPH NODE                                                 41
                                           clus
vv                                          DEL PEAK  1(1P36.31) WILD-TYPE
  DISTANT METASTASIS                                                    22
  PRIMARY TUMOR                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             48
  REGIONAL LYMPH NODE                                                  138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  1(1P36.31) MUTATED             1       1      10        2        5
  DEL PEAK  1(1P36.31) WILD-TYPE           9       5      13        8       20
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  1(1P36.31) MUTATED          4         2         2         1
  DEL PEAK  1(1P36.31) WILD-TYPE       13         8        12         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  1(1P36.31) MUTATED          11          0          5         16
  DEL PEAK  1(1P36.31) WILD-TYPE        21         14         18         32
                                vv
clus                             STAGE IV
  DEL PEAK  1(1P36.31) MUTATED          4
  DEL PEAK  1(1P36.31) WILD-TYPE        8
D24V5, multiclass
             clus
vv            DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  I OR II NOS                            1                              9
  STAGE 0                                1                              5
  STAGE I                               10                             13
  STAGE IA                               2                              8
  STAGE IB                               5                             20
  STAGE II                               4                             13
  STAGE IIA                              2                              8
  STAGE IIB                              2                             12
  STAGE IIC                              1                              9
  STAGE III                             11                             21
  STAGE IIIA                             0                             14
  STAGE IIIB                             5                             18
  STAGE IIIC                            16                             32
  STAGE IV                               4                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK  1(1P36.31) MUTATED      17 18 11 14
  DEL PEAK  1(1P36.31) WILD-TYPE    36 42 44 43
D24V6, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T0+T1                           17                             36
  T2                              18                             42
  T3                              11                             44
  T4                              14                             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK  1(1P36.31) MUTATED    35  12   7  10
  DEL PEAK  1(1P36.31) WILD-TYPE 106  39  25  27
D24V7, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                           35                            106
  N1                           12                             39
  N2                            7                             25
  N3                           10                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK  1(1P36.31) MUTATED    60   1   2   0   1
  DEL PEAK  1(1P36.31) WILD-TYPE 192   3   0   2   4
D24V8, multiclass
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  M0                            60                            192
  M1                             1                              3
  M1A                            2                              0
  M1B                            0                              2
  M1C                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED   25 18
  DEL PEAK  1(1P36.31) WILD-TYPE 79 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     25   18
  DEL PEAK  1(1P36.31) WILD-TYPE   79   54
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                            25                             79
  YES                           18                             54
[1] 2 2
[1] FALSE
D24V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     9  59
  DEL PEAK  1(1P36.31) WILD-TYPE  25 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      9   59
  DEL PEAK  1(1P36.31) WILD-TYPE   25  188
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                             9                             25
  YES                           59                            188
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    30  38
  DEL PEAK  1(1P36.31) WILD-TYPE  78 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     30   38
  DEL PEAK  1(1P36.31) WILD-TYPE   78  135
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           30                             78
  MALE                             38                            135
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED       1                         0    67
  DEL PEAK  1(1P36.31) WILD-TYPE     4                         1   208
D24V13, multiclass
                           clus
vv                          DEL PEAK  1(1P36.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               67
                           clus
vv                          DEL PEAK  1(1P36.31) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     0  67
  DEL PEAK  1(1P36.31) WILD-TYPE   3 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      0   67
  DEL PEAK  1(1P36.31) WILD-TYPE    3  207
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            207
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  2(1P22.1) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P22.1) MUTATED    37  33
  DEL PEAK  2(1P22.1) WILD-TYPE 100 100
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           70                           200 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           33                           100 
$`DEL PEAK  2(1P22.1) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JC 
      111.09        28.08        22.55        10.29        85.32        69.90 
TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       11.41        56.19        64.44        61.38        13.32         9.34 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z3 TCGA-DA-A1I0 
        5.39        52.01         1.55         6.97         2.89        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 
       13.68        36.69        25.15         4.93        17.56        14.83 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20H 
        0.20         0.00        10.55         8.12        36.07         9.21 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2GC TCGA-EE-A2GE 
       37.97        11.15         8.84         6.48        34.29        34.92 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB 
       30.84         1.15       111.78        26.99        27.16       122.73 
TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C 
        3.68        12.72         3.22        31.40        12.95         3.78 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG 
        3.52        13.45        28.60        36.07         1.87        12.62 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1Z0 
       11.74        22.49         1.71         4.90         3.45        23.80 
TCGA-FS-A1Z7 TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 
        7.33        12.92        49.15        40.64        27.39        14.20 
TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A26D TCGA-GN-A4U9 
        0.16        24.85        14.70        10.65 

$`DEL PEAK  2(1P22.1) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA 
       16.47         8.52        32.42        70.16       110.79        45.83 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF 
       81.24         8.38        21.14        88.50        68.22        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        92.42        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML 
       15.25        46.98        46.32        82.29        24.00         6.31 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        26.37        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        95.38        47.87 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       23.11         4.01         9.90        11.31        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       48.79        35.80        51.12        39.19         9.99        44.52 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH 
       22.36         6.64        19.36         7.00        13.15         0.13 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        0.00        13.22         0.20        11.57         6.31         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        1.35        12.20         5.13         4.31         4.34         5.13 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        1.18         7.99         9.90        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        1.08        27.12         9.50        12.03         8.09         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI 
        9.67         8.94        39.39        17.98        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       19.43        16.01        35.54        28.31        33.83         5.42 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       14.56        63.42       111.91        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
       29.65        23.05         5.56       124.31        25.84        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        15.95        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       22.22        27.35         0.46        13.94        33.60        18.61 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F 
       38.40         5.72        76.41        25.18        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      114.15        34.88         4.21        42.84        34.68         9.57 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       17.72        78.44        11.80         1.51        13.08         9.04 
TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
        6.58        18.41        85.74         6.71         3.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       64.47        11.01        14.24        15.52         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
       12.89        47.38        52.08         8.65         8.81         8.68 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
        0.82         5.23        53.85         3.22         7.36        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 
        0.13         0.43         9.90         7.23        12.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
       84.72        10.13        16.24        15.42        12.16        11.84 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                            0                             0 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       122.73                        124.31 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       13.385                        14.580 
[1] "0.0 - 122.7 (13.4)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1"  
D25V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P22.1) MUTATED    38  33
  DEL PEAK  2(1P22.1) WILD-TYPE 104 101
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           71                           205 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           33                           101 
$`DEL PEAK  2(1P22.1) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JC 
      112.04        28.08        31.59        43.43       103.10        69.90 
TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       11.87        56.19        66.08        86.93        60.23         9.34 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z3 TCGA-DA-A1I0 
       21.47       135.75       166.19         7.43         3.25        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 
      176.55        61.18        53.92        65.92       215.44        15.68 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B 
       10.16        35.01         3.55        27.22        94.98       109.64 
TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2GC 
      168.26        47.84        13.97        14.47       345.96        67.43 
TCGA-EE-A2GE TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
      135.95       101.95        14.30       144.76       248.65       136.47 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A197 
      122.73         3.68       138.81       172.18        31.40        13.94 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A2ND 
       48.89        12.59       131.51        61.05        37.25        23.34 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FS-A1YX 
       31.27        32.05        46.98        33.21         4.90        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
      202.65         7.79        47.38       148.80        53.16        49.48 
TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A26D TCGA-GN-A4U9 
      174.84         0.16       120.46        39.58        12.62 

$`DEL PEAK  2(1P22.1) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA 
       16.57        16.67       112.57        71.80       133.25        90.90 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF 
       95.74        65.49        23.77       115.53       168.00        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10       171.58        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98        46.32       166.52        24.53        13.87 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       110.93       137.92 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A1IC 
      117.21       194.83        35.93       107.34        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN 
       28.60        10.49        13.87        17.85        45.11        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        6.35        12.20        29.82         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       151.27        78.87        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       63.35        80.61        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       44.35        18.61        56.42        37.35        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       58.75        47.54       314.56       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       54.74        79.66        75.48        90.97        13.91        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       203.05       167.90        47.54        43.23       103.56 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       41.59        53.26       124.31        25.84        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       23.47       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       27.35        33.40       101.79       148.08        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        98.40        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
      152.35         6.44        44.05       162.08        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       79.99        43.82        20.15        16.37       247.04        80.32 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       92.98       174.21       210.08        15.16         7.00       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      228.59        20.91        28.08        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
       53.52        40.27        15.45         9.70        32.75        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZY 
      101.26        74.73       133.55        11.41        26.56        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67        28.73        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 
        2.40         9.90         7.23        14.04       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-OD-A75X 
       10.13        64.44        62.79        32.48        46.36       294.77 
TCGA-QB-A6FS 
        6.67 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                         0.16                          0.20 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       345.96                        357.37 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                        48.89                         47.54 
[1] "0.2 - 346.0 (48.9)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.1"
D25V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  2(1P22.1) MUTATED                    7             0
  DEL PEAK  2(1P22.1) WILD-TYPE                 30             4
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  2(1P22.1) MUTATED                                          16
  DEL PEAK  2(1P22.1) WILD-TYPE                                        44
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  2(1P22.1) MUTATED                    47
  DEL PEAK  2(1P22.1) WILD-TYPE                 132
D25V4, multiclass
                                           clus
vv                                          DEL PEAK  2(1P22.1) MUTATED
  DISTANT METASTASIS                                                  7
  PRIMARY TUMOR                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          16
  REGIONAL LYMPH NODE                                                47
                                           clus
vv                                          DEL PEAK  2(1P22.1) WILD-TYPE
  DISTANT METASTASIS                                                   30
  PRIMARY TUMOR                                                         4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            44
  REGIONAL LYMPH NODE                                                 132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  2(1P22.1) MUTATED             0       0       8        1        4
  DEL PEAK  2(1P22.1) WILD-TYPE          10       6      15        9       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  2(1P22.1) MUTATED          6         0         3         2
  DEL PEAK  2(1P22.1) WILD-TYPE       11        10        11         8
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  2(1P22.1) MUTATED          14          0         10         15
  DEL PEAK  2(1P22.1) WILD-TYPE        18         14         13         33
                               vv
clus                            STAGE IV
  DEL PEAK  2(1P22.1) MUTATED          4
  DEL PEAK  2(1P22.1) WILD-TYPE        8
D25V5, multiclass
             clus
vv            DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  I OR II NOS                           0                            10
  STAGE 0                               0                             6
  STAGE I                               8                            15
  STAGE IA                              1                             9
  STAGE IB                              4                            21
  STAGE II                              6                            11
  STAGE IIA                             0                            10
  STAGE IIB                             3                            11
  STAGE IIC                             2                             8
  STAGE III                            14                            18
  STAGE IIIA                            0                            14
  STAGE IIIB                           10                            13
  STAGE IIIC                           15                            33
  STAGE IV                              4                             8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  2(1P22.1) MUTATED      15 18 14 15
  DEL PEAK  2(1P22.1) WILD-TYPE    38 42 41 42
D25V6, multiclass
       clus
vv      DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  T0+T1                          15                            38
  T2                             18                            42
  T3                             14                            41
  T4                             15                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  2(1P22.1) MUTATED    28  18  10  10
  DEL PEAK  2(1P22.1) WILD-TYPE 113  33  22  27
D25V7, multiclass
    clus
vv   DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  N0                          28                           113
  N1                          18                            33
  N2                          10                            22
  N3                          10                            27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  DEL PEAK  2(1P22.1) MUTATED    62   0   2   1   1
  DEL PEAK  2(1P22.1) WILD-TYPE 190   4   0   1   4
D25V8, multiclass
     clus
vv    DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  M0                           62                           190
  M1                            0                             4
  M1A                           2                             0
  M1B                           1                             1
  M1C                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P22.1) MUTATED   20 23
  DEL PEAK  2(1P22.1) WILD-TYPE 84 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     20   23
  DEL PEAK  2(1P22.1) WILD-TYPE   84   49
     clus
vv    DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  NO                           20                            84
  YES                          23                            49
[1] 2 2
[1] FALSE
D25V10, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED     9  62
  DEL PEAK  2(1P22.1) WILD-TYPE  25 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED      9   62
  DEL PEAK  2(1P22.1) WILD-TYPE   25  185
     clus
vv    DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  NO                            9                            25
  YES                          62                           185
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED    31  40
  DEL PEAK  2(1P22.1) WILD-TYPE  77 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     31   40
  DEL PEAK  2(1P22.1) WILD-TYPE   77  133
        clus
vv       DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  FEMALE                          31                            77
  MALE                            40                           133
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P22.1) MUTATED       2                         0    69
  DEL PEAK  2(1P22.1) WILD-TYPE     3                         1   206
D25V13, multiclass
                           clus
vv                          DEL PEAK  2(1P22.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              69
                           clus
vv                          DEL PEAK  2(1P22.1) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED     0  70
  DEL PEAK  2(1P22.1) WILD-TYPE   3 204
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED      0   70
  DEL PEAK  2(1P22.1) WILD-TYPE    3  204
                        clus
vv                       DEL PEAK  2(1P22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          70
                        clus
vv                       DEL PEAK  2(1P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           204
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  3(2Q37.3) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q37.3) MUTATED    29  38
  DEL PEAK  3(2Q37.3) WILD-TYPE 108  95
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           67                           203 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           38                            95 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-D3-A1QA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3C6 
       45.83        69.90        11.41         7.50         6.31        15.25 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51T TCGA-D9-A6EA 
       82.29       103.59        26.37        17.72        13.94        11.31 
TCGA-DA-A1I0 TCGA-DA-A1IA TCGA-EB-A44R TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C 
       10.03         4.93         0.20         8.12        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        5.13         9.21         1.18        37.97        11.15        38.63 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR 
       12.03         8.09         8.94        34.29        47.21         1.15 
TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AF 
        2.70         7.96        63.42       111.78        27.16        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 
       15.95         3.22        22.22         0.46        31.40        12.95 
TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV 
        3.78        34.68        17.72         1.87         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        1.71        85.74        64.47         3.45        11.01        23.80 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       12.92        47.38         8.65         5.23        53.85         7.36 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        0.20         0.13        24.85        31.33        10.13        16.24 
TCGA-GN-A26D 
       14.70 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
       21.14        88.50        68.22        30.87        36.16        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        64.44        45.11       114.67        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV 
       61.38        13.32        24.00         6.31         9.34         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R 
       80.22        42.71        15.09        41.10         8.84        20.48 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       95.38        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01         2.89         9.90        13.22        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.13         0.00         0.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       13.22         0.20        11.57        10.55         6.31         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29B 
        1.35        12.20         5.13         4.31         7.99         9.90 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R 
        8.55         4.41         1.08        27.12         9.50         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       49.22        23.90         9.67        39.39        17.98        34.92 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       30.84         5.42        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       98.27         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       14.56       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       29.65        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
        3.68        30.15        12.72        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       16.14        27.35        13.94        33.60        18.61        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        5.72        76.41        25.18         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        9.57        36.07        78.44        11.80         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 
       12.62        11.74         9.04        18.41         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.58         5.36        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       30.87        12.89        52.08         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
        8.68        27.39         0.82         3.22        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV 
       10.78         5.98         6.41         2.27         0.99         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A268 
        0.43         9.90         7.23        12.85        84.72        15.42 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        11.84        10.65        11.05         5.79 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       111.78                        124.31 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        12.92                         14.60 
[1] "0.1 - 111.8 (12.9)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1.4"
D26V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q37.3) MUTATED    31  38
  DEL PEAK  3(2Q37.3) WILD-TYPE 111  96
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           69                           207 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           38                            96 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-D3-A1QA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3C6 
       90.90        69.90        11.87       113.52        12.10        58.06 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51T TCGA-D9-A148 
      166.52       103.59        39.75        18.38        15.06       151.53 
TCGA-D9-A149 TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-DA-A1IA TCGA-EB-A44R TCGA-EE-A180 
       54.67        25.18        20.38        65.92        10.16        94.98 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C 
      109.64       151.27        78.87       168.26        13.55        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A6 TCGA-EE-A2GC 
       13.97        39.62        56.42        37.35        58.75        67.43 
TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
      208.04        14.30        28.83        16.96        96.23       144.76 
TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE 
      136.47        13.81        23.47       172.18        53.19        33.40 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A2ND 
       31.40        13.94        48.89       162.08       148.18        23.34 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX 
       80.32        46.98        33.21       174.21       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZZ 
      228.59       202.65        47.38       101.26       133.55        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
       77.82        66.67         0.20        47.54       120.46       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D 
       10.13        64.44        39.58 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
       23.77       115.53       168.00        48.76        42.08       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        66.08        45.11       130.72        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV 
       86.93        60.23        24.53        13.87         9.34        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R 
      161.85        43.69        40.14       131.90        10.03        51.68 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      110.93       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC 
        3.65         6.41        11.34         3.25         9.90        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        48.89        36.03       117.21       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        61.18        53.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       28.60        10.49       215.44        15.68        13.87        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       45.11        35.01         3.55        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H 
       68.15         4.96        63.35        80.61        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        2.60        44.35        18.61        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.29        47.54       314.56       135.95        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
       55.59        44.88        94.82        21.67       129.27        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML 
       61.51        47.28       103.27       103.20       204.66       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       103.56        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD 
      138.81       127.20        36.95        64.08        34.32        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      101.79       148.08        35.44        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05        44.05        50.89        37.25 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        43.82        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
      247.04        92.98         4.90       210.08        15.16         7.00 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
       53.52        40.27        15.45         9.70        32.75        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.09        50.14        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45        77.88        22.92         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
        7.23        14.04        84.72        62.79        32.48        46.36 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                         0.20                          0.16 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       228.59                        357.37 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        56.42                         46.36 
[1] "0.2 - 228.6 (56.4)" "0.2 - 357.4 (46.4)"
[1] "hr=" "1"  
D26V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  3(2Q37.3) MUTATED                   12             1
  DEL PEAK  3(2Q37.3) WILD-TYPE                 25             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  3(2Q37.3) MUTATED                                          19
  DEL PEAK  3(2Q37.3) WILD-TYPE                                        41
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  3(2Q37.3) MUTATED                    36
  DEL PEAK  3(2Q37.3) WILD-TYPE                 143
D26V4, multiclass
                                           clus
vv                                          DEL PEAK  3(2Q37.3) MUTATED
  DISTANT METASTASIS                                                 12
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          19
  REGIONAL LYMPH NODE                                                36
                                           clus
vv                                          DEL PEAK  3(2Q37.3) WILD-TYPE
  DISTANT METASTASIS                                                   25
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            41
  REGIONAL LYMPH NODE                                                 143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  3(2Q37.3) MUTATED             2       1       6        2        6
  DEL PEAK  3(2Q37.3) WILD-TYPE           8       5      17        8       19
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  3(2Q37.3) MUTATED          5         2         5         2
  DEL PEAK  3(2Q37.3) WILD-TYPE       12         8         9         8
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  3(2Q37.3) MUTATED           9          4          6          7
  DEL PEAK  3(2Q37.3) WILD-TYPE        23         10         17         41
                               vv
clus                            STAGE IV
  DEL PEAK  3(2Q37.3) MUTATED          4
  DEL PEAK  3(2Q37.3) WILD-TYPE        8
D26V5, multiclass
             clus
vv            DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  I OR II NOS                           2                             8
  STAGE 0                               1                             5
  STAGE I                               6                            17
  STAGE IA                              2                             8
  STAGE IB                              6                            19
  STAGE II                              5                            12
  STAGE IIA                             2                             8
  STAGE IIB                             5                             9
  STAGE IIC                             2                             8
  STAGE III                             9                            23
  STAGE IIIA                            4                            10
  STAGE IIIB                            6                            17
  STAGE IIIC                            7                            41
  STAGE IV                              4                             8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  3(2Q37.3) MUTATED       9 14 16 17
  DEL PEAK  3(2Q37.3) WILD-TYPE    44 46 39 40
D26V6, multiclass
       clus
vv      DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  T0+T1                           9                            44
  T2                             14                            46
  T3                             16                            39
  T4                             17                            40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  3(2Q37.3) MUTATED    39  12   7   5
  DEL PEAK  3(2Q37.3) WILD-TYPE 102  39  25  32
D26V7, multiclass
    clus
vv   DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  N0                          39                           102
  N1                          12                            39
  N2                           7                            25
  N3                           5                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  DEL PEAK  3(2Q37.3) MUTATED    58   1   2   1   1
  DEL PEAK  3(2Q37.3) WILD-TYPE 194   3   0   1   4
D26V8, multiclass
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  M0                           58                           194
  M1                            1                             3
  M1A                           2                             0
  M1B                           1                             1
  M1C                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q37.3) MUTATED   30 15
  DEL PEAK  3(2Q37.3) WILD-TYPE 74 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     30   15
  DEL PEAK  3(2Q37.3) WILD-TYPE   74   57
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  NO                           30                            74
  YES                          15                            57
[1] 2 2
[1] FALSE
D26V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED     6  63
  DEL PEAK  3(2Q37.3) WILD-TYPE  28 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      6   63
  DEL PEAK  3(2Q37.3) WILD-TYPE   28  184
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  NO                            6                            28
  YES                          63                           184
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED    27  42
  DEL PEAK  3(2Q37.3) WILD-TYPE  81 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     27   42
  DEL PEAK  3(2Q37.3) WILD-TYPE   81  131
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  FEMALE                          27                            81
  MALE                            42                           131
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q37.3) MUTATED       1                         0    68
  DEL PEAK  3(2Q37.3) WILD-TYPE     4                         1   207
D26V13, multiclass
                           clus
vv                          DEL PEAK  3(2Q37.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              68
                           clus
vv                          DEL PEAK  3(2Q37.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED     2  66
  DEL PEAK  3(2Q37.3) WILD-TYPE   1 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      2   66
  DEL PEAK  3(2Q37.3) WILD-TYPE    1  208
                        clus
vv                       DEL PEAK  3(2Q37.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          66
                        clus
vv                       DEL PEAK  3(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           208
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  4(3P24.3) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(3P24.3) MUTATED    30  23
  DEL PEAK  4(3P24.3) WILD-TYPE 107 110
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                           53                           217 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                           23                           110 
$`DEL PEAK  4(3P24.3) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC 
      111.09        32.42       110.79        85.32        88.50        69.90 
TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A5GL TCGA-D3-A5GU 
        7.50        56.19        15.25        46.98        95.38        23.11 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 
        9.90        11.31        48.79        35.80        13.68        44.52 
TCGA-DA-A1I7 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29G 
       36.69         0.20        10.55         4.34         5.13         8.55 
TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD 
       12.03         2.43        47.21        98.27         2.70         9.53 
TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19Q 
      124.31         3.22        21.60        11.90        34.88         9.57 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 
       36.07         1.87        12.62        85.74         6.71         5.36 
TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FW-A3TU 
        3.45        47.38         8.65        49.15        14.20         0.13 
TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A4U9 
        0.16        12.85        24.85        16.24        10.65 

$`DEL PEAK  4(3P24.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.47         8.52        70.16        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD 
       81.24        10.29         8.38        21.14        68.22        11.41 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
       30.87        36.16         6.31        92.42        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      114.67        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
        6.31         9.34       103.59        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 
       13.94        52.01        47.87         1.55         6.97         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        2.89        13.22        14.60        51.12        10.03        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.13         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
        0.00        13.22         0.20        11.57         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       38.63         4.41         1.08        27.12         9.50         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         6.48         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       34.98        36.33         8.84         6.18        47.51        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.05         5.56       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        15.95        12.72        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
        3.78         3.52        11.11       114.15         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       28.60        42.84        34.68        17.72        78.44        11.80 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        1.51        13.08        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
        1.71        18.41         4.90         3.58        64.47        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
       12.92        12.89        52.08         8.81        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       27.39         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
        0.99         0.43         9.90         7.23        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X 
       10.13        15.42        12.16        14.70        11.84        11.05 
TCGA-QB-A6FS 
        5.79 

  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                       124.31                        122.73 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                        14.20                         13.94 
[1] "0.1 - 124.3 (14.2)" "0.0 - 122.7 (13.9)"
[1] "hr=" "1.4"
D27V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(3P24.3) MUTATED    31  23
  DEL PEAK  4(3P24.3) WILD-TYPE 111 111
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                           54                           222 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                           23                           111 
$`DEL PEAK  4(3P24.3) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC 
      112.04       112.57       133.25       103.10       115.53        69.90 
TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A5GL TCGA-D3-A5GU 
      113.52        56.19        58.06        46.98       110.93       125.19 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 
        9.90        25.18        48.89        36.03       176.55       107.34 
TCGA-DA-A1I7 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20F 
       61.18        10.16         3.55        27.22       151.27        78.87 
TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2M7 
       72.07        56.42        25.87       208.04       129.27        28.83 
TCGA-EE-A2MD TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19E TCGA-ER-A19H 
       47.28       124.31       172.18        64.08        13.02       152.35 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A44A TCGA-FR-A729 
       50.89        37.25        23.34        31.27       174.21       210.08 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A4F8 
        7.00        48.59       101.26       133.55       148.80       174.84 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A4U9 
       47.54         0.16        14.04       120.46        64.44        12.62 

$`DEL PEAK  4(3P24.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.57        16.67        71.80        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD 
       95.74        43.43        65.49        23.77       168.00        11.87 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
       48.76        42.08        12.10       171.58        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 
       15.06       135.75       137.92       166.19         7.43       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       54.67         3.65         6.41        11.34         3.25        66.25 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 
       22.95       117.21        20.38       194.83        35.93        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       15.68        13.87        17.85        45.11        35.01        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        6.35        12.20        29.82         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H 
       14.70        26.89        68.15         4.96       109.64       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       32.19         2.60        44.35        18.61        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92       345.96       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      135.95        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       94.82        21.67        19.76        61.51       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
       23.47       138.81       127.20        36.95        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       12.59        26.37       268.93         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       44.05       162.08       148.18        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.37        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       92.98         4.90        15.16       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       23.93        74.73        11.41        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.40         9.90         7.23       117.93        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        32.48        39.58        46.36       294.77         6.67 

  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                         0.16                          0.20 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                       210.08                        357.37 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                        64.26                         45.11 
[1] "0.2 - 210.1 (64.3)" "0.2 - 357.4 (45.1)"
[1] "hr=" "1.4"
D27V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  4(3P24.3) MUTATED                    6             2
  DEL PEAK  4(3P24.3) WILD-TYPE                 31             2
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  4(3P24.3) MUTATED                                          10
  DEL PEAK  4(3P24.3) WILD-TYPE                                        50
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  4(3P24.3) MUTATED                    36
  DEL PEAK  4(3P24.3) WILD-TYPE                 143
D27V4, multiclass
                                           clus
vv                                          DEL PEAK  4(3P24.3) MUTATED
  DISTANT METASTASIS                                                  6
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          10
  REGIONAL LYMPH NODE                                                36
                                           clus
vv                                          DEL PEAK  4(3P24.3) WILD-TYPE
  DISTANT METASTASIS                                                   31
  PRIMARY TUMOR                                                         2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            50
  REGIONAL LYMPH NODE                                                 143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  4(3P24.3) MUTATED             2       1       7        0        6
  DEL PEAK  4(3P24.3) WILD-TYPE           8       5      16       10       19
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  4(3P24.3) MUTATED          4         0         1         1
  DEL PEAK  4(3P24.3) WILD-TYPE       13        10        13         9
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  4(3P24.3) MUTATED           7          5          5          9
  DEL PEAK  4(3P24.3) WILD-TYPE        25          9         18         39
                               vv
clus                            STAGE IV
  DEL PEAK  4(3P24.3) MUTATED          1
  DEL PEAK  4(3P24.3) WILD-TYPE       11
D27V5, multiclass
             clus
vv            DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE
  I OR II NOS                           2                             8
  STAGE 0                               1                             5
  STAGE I                               7                            16
  STAGE IA                              0                            10
  STAGE IB                              6                            19
  STAGE II                              4                            13
  STAGE IIA                             0                            10
  STAGE IIB                             1                            13
  STAGE IIC                             1                             9
  STAGE III                             7                            25
  STAGE IIIA                            5                             9
  STAGE IIIB                            5                            18
  STAGE IIIC                            9                            39
  STAGE IV                              1                            11
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  4(3P24.3) MUTATED      16 12 11  5
  DEL PEAK  4(3P24.3) WILD-TYPE    37 48 44 52
D27V6, multiclass
       clus
vv      DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE
  T0+T1                          16                            37
  T2                             12                            48
  T3                             11                            44
  T4                              5                            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  4(3P24.3) MUTATED    24  13   8   5
  DEL PEAK  4(3P24.3) WILD-TYPE 117  38  24  32
D27V7, multiclass
    clus
vv   DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE
  N0                          24                           117
  N1                          13                            38
  N2                           8                            24
  N3                           5                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  DEL PEAK  4(3P24.3) MUTATED    50   0   0   0   1
  DEL PEAK  4(3P24.3) WILD-TYPE 202   4   2   2   4
D27V8, multiclass
     clus
vv    DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE
  M0                           50                           202
  M1                            0                             4
  M1A                           0                             2
  M1B                           0                             2
  M1C                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                               cls
clus                             0  1
  DEL PEAK  4(3P24.3) MUTATED   19 12
  DEL PEAK  4(3P24.3) WILD-TYPE 85 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P24.3) MUTATED     19   12
  DEL PEAK  4(3P24.3) WILD-TYPE   85   60
     clus
vv    DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE
  NO                           19                            85
  YES                          12                            60
[1] 2 2
[1] FALSE
D27V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P24.3) MUTATED     7  47
  DEL PEAK  4(3P24.3) WILD-TYPE  27 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P24.3) MUTATED      7   47
  DEL PEAK  4(3P24.3) WILD-TYPE   27  200
     clus
vv    DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE
  NO                            7                            27
  YES                          47                           200
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P24.3) MUTATED    25  29
  DEL PEAK  4(3P24.3) WILD-TYPE  83 144
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P24.3) MUTATED     25   29
  DEL PEAK  4(3P24.3) WILD-TYPE   83  144
        clus
vv       DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE
  FEMALE                          25                            83
  MALE                            29                           144
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3P24.3) MUTATED       2                         0    52
  DEL PEAK  4(3P24.3) WILD-TYPE     3                         1   223
D27V13, multiclass
                           clus
vv                          DEL PEAK  4(3P24.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              52
                           clus
vv                          DEL PEAK  4(3P24.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P24.3) MUTATED     0  53
  DEL PEAK  4(3P24.3) WILD-TYPE   3 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P24.3) MUTATED      0   53
  DEL PEAK  4(3P24.3) WILD-TYPE    3  221
                        clus
vv                       DEL PEAK  4(3P24.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       DEL PEAK  4(3P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           221
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  5(3Q23) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  5(3Q23) MUTATED    24  22
  DEL PEAK  5(3Q23) WILD-TYPE 113 111
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                         46                         224 
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                         22                         111 
$`DEL PEAK  5(3Q23) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EA 
       32.42       110.79         7.50        23.11         9.90        11.31 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y 
       13.68        44.52        36.69         0.00         0.20        10.55 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29X 
        4.34         1.18         8.55         4.41        12.03         8.09 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2MR TCGA-EE-A3J3 
       34.29        47.21        19.43        33.83        29.65         3.22 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       33.60        18.61        12.95        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       34.88         4.21         5.36         3.45        12.92        47.38 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 
        7.36        14.20         2.27         0.20         0.13        24.85 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
       31.33        16.24        15.42        10.65 

$`DEL PEAK  5(3Q23) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47         8.52       111.09        70.16        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH 
       88.50        68.22        69.90        11.41        30.87        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       20.48        13.94        95.38        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        6.97         4.01         2.89        13.22        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 
       35.80        51.12        10.03        39.19         9.99        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN 
       14.83        13.15         0.20         0.13         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       11.57         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        5.13         4.31        36.07         5.13         9.21         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M 
        9.90        37.97        11.15        38.63         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        9.50         8.09         8.84         9.99         6.48         2.43 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.68        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       39.39        17.98        34.92        30.08        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
        3.68        30.15        13.81        15.95        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       13.94        31.40        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
        3.78         3.52        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       22.49         1.71        18.41        85.74         4.90         6.71 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        3.58        64.47        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       11.08         7.17        30.87        12.89        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23        53.85         3.22        28.73        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        6.41         0.99         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       12.85        84.72        10.13        12.16        14.70        11.84 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                          0                           0 
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                     114.15                      124.31 
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                     12.475                      14.650 
[1] "0.0 - 114.2 (12.5)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1.1"
D28V2, survival
                             sevent
clus2                           0   1
  DEL PEAK  5(3Q23) MUTATED    24  22
  DEL PEAK  5(3Q23) WILD-TYPE 118 112
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                         46                         230 
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                         22                         112 
$`DEL PEAK  5(3Q23) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EA 
      112.57       133.25       113.52       125.19         9.90        25.18 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y 
      176.55       107.34        61.18        35.01        12.20        27.22 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29X 
      151.27        13.55        72.07        32.19        56.42        17.92 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2MR TCGA-EE-A3J3 
       67.43       208.04        89.33        90.97       103.56       172.18 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
      148.08        35.44        13.94        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      152.35         6.44         7.00        48.59        47.38       101.26 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 
       66.67       174.84        77.88         0.20        47.54       120.46 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
      117.93        64.44        62.79        12.62 

$`DEL PEAK  5(3Q23) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57        16.67       112.04        71.80        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH 
      115.53       168.00        69.90        11.87        48.76        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       51.68        15.06       110.93       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
        7.43       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        3.25        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       194.83        35.93        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       10.16        17.85        45.11         3.55        52.01         6.35 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       68.15         4.96       109.64        78.87       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M 
       80.61        47.84        13.97        39.62         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        37.35        14.47        55.92       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
      171.55        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       47.54       314.56       135.95        48.72        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
        3.68        54.51        13.81        23.47       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      101.79        31.40        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       48.89        12.59       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98        33.21        92.98       174.21         4.90       210.08 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.16       216.92       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       15.45         9.70        32.75        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        50.14        28.73        12.43        26.73 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       49.45        22.92         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       14.04        84.72        10.13        32.48        39.58        46.36 
TCGA-OD-A75X TCGA-QB-A6FS 
      294.77         6.67 

  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                       0.20                        0.16 
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                     268.93                      357.37 
  DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE 
                     65.555                      46.900 
[1] "0.2 - 268.9 (65.6)" "0.2 - 357.4 (46.9)"
[1] "hr=" "1.2"
D28V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  5(3Q23) MUTATED                    4             2
  DEL PEAK  5(3Q23) WILD-TYPE                 33             2
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  5(3Q23) MUTATED                                          11
  DEL PEAK  5(3Q23) WILD-TYPE                                        49
                             vv
clus                          REGIONAL LYMPH NODE
  DEL PEAK  5(3Q23) MUTATED                    28
  DEL PEAK  5(3Q23) WILD-TYPE                 151
D28V4, multiclass
                                           clus
vv                                          DEL PEAK  5(3Q23) MUTATED
  DISTANT METASTASIS                                                4
  PRIMARY TUMOR                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        11
  REGIONAL LYMPH NODE                                              28
                                           clus
vv                                          DEL PEAK  5(3Q23) WILD-TYPE
  DISTANT METASTASIS                                                 33
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          49
  REGIONAL LYMPH NODE                                               151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  5(3Q23) MUTATED             1       1       6        2        5
  DEL PEAK  5(3Q23) WILD-TYPE           9       5      17        8       20
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  5(3Q23) MUTATED          0         2         2         1         2
  DEL PEAK  5(3Q23) WILD-TYPE       17         8        12         9        30
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  5(3Q23) MUTATED            4          3          6        4
  DEL PEAK  5(3Q23) WILD-TYPE         10         20         42        8
D28V5, multiclass
             clus
vv            DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE
  I OR II NOS                         1                           9
  STAGE 0                             1                           5
  STAGE I                             6                          17
  STAGE IA                            2                           8
  STAGE IB                            5                          20
  STAGE II                            0                          17
  STAGE IIA                           2                           8
  STAGE IIB                           2                          12
  STAGE IIC                           1                           9
  STAGE III                           2                          30
  STAGE IIIA                          4                          10
  STAGE IIIB                          3                          20
  STAGE IIIC                          6                          42
  STAGE IV                            4                           8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK  5(3Q23) MUTATED       7 13  5  9
  DEL PEAK  5(3Q23) WILD-TYPE    46 47 50 48
D28V6, multiclass
       clus
vv      DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE
  T0+T1                         7                          46
  T2                           13                          47
  T3                            5                          50
  T4                            9                          48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  5(3Q23) MUTATED    28   5   4   6
  DEL PEAK  5(3Q23) WILD-TYPE 113  46  28  31
D28V7, multiclass
    clus
vv   DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE
  N0                        28                         113
  N1                         5                          46
  N2                         4                          28
  N3                         6                          31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  DEL PEAK  5(3Q23) MUTATED    39   2   0   0   2
  DEL PEAK  5(3Q23) WILD-TYPE 213   2   2   2   3
D28V8, multiclass
     clus
vv    DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE
  M0                         39                         213
  M1                          2                           2
  M1A                         0                           2
  M1B                         0                           2
  M1C                         2                           3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                             cls
clus                           0  1
  DEL PEAK  5(3Q23) MUTATED   19 12
  DEL PEAK  5(3Q23) WILD-TYPE 85 60
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3Q23) MUTATED     19   12
  DEL PEAK  5(3Q23) WILD-TYPE   85   60
     clus
vv    DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE
  NO                         19                          85
  YES                        12                          60
[1] 2 2
[1] FALSE
D28V10, binary
                             cls
clus                            0   1
  DEL PEAK  5(3Q23) MUTATED     3  43
  DEL PEAK  5(3Q23) WILD-TYPE  31 204
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3Q23) MUTATED      3   43
  DEL PEAK  5(3Q23) WILD-TYPE   31  204
     clus
vv    DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE
  NO                          3                          31
  YES                        43                         204
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, binary
                             cls
clus                            0   1
  DEL PEAK  5(3Q23) MUTATED    18  28
  DEL PEAK  5(3Q23) WILD-TYPE  90 145
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3Q23) MUTATED     18   28
  DEL PEAK  5(3Q23) WILD-TYPE   90  145
        clus
vv       DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE
  FEMALE                        18                          90
  MALE                          28                         145
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3Q23) MUTATED       2                         0    44
  DEL PEAK  5(3Q23) WILD-TYPE     3                         1   231
D28V13, multiclass
                           clus
vv                          DEL PEAK  5(3Q23) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            44
                           clus
vv                          DEL PEAK  5(3Q23) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             231
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                             cls
clus                            0   1
  DEL PEAK  5(3Q23) MUTATED     0  44
  DEL PEAK  5(3Q23) WILD-TYPE   3 230
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3Q23) MUTATED      0   44
  DEL PEAK  5(3Q23) WILD-TYPE    3  230
                        clus
vv                       DEL PEAK  5(3Q23) MUTATED DEL PEAK  5(3Q23) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                        44                         230
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q34.3) MUTATED   40 35
  DEL PEAK  6(4Q34.3) WILD-TYPE 97 98
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           75                           195 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           35                            98 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JN 
       16.47       111.09        28.08        88.50        11.41        56.19 
TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F 
       64.44        46.98        61.38       103.59         5.39        42.71 
TCGA-D3-A51N TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I7 
        8.84         9.90        13.22        35.80        51.12        36.69 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       17.56        14.83         0.20        10.55         8.12         1.12 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
       36.07         9.21        37.97        27.12         6.48         8.68 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
        8.09         9.67         8.94        47.21        30.08        28.31 
TCGA-EE-A2GO TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ 
       30.84        36.33         8.84        98.27        56.02        21.60 
TCGA-EE-A2MT TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       23.05        15.95        22.92        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
        0.46        31.40        12.95        25.18         3.52        11.90 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV 
       36.07         1.87        12.62        11.74         6.58        22.49 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC 
        3.58         5.36        23.80        15.52         7.30        20.38 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FW-A3I3 TCGA-FW-A3TU 
       19.53        11.08         7.17        12.92         0.20         0.13 
TCGA-GF-A6C8 TCGA-GN-A266 TCGA-GN-A4U9 
       12.85        10.13        10.65 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
        8.52        32.42        70.16       110.79        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       81.24        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        30.87         7.50        36.16         6.31        92.42 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       45.11       114.67        15.25        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H 
       24.00         6.31         9.34        26.37        80.22        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       41.10        17.72        20.48        13.94        95.38        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.31        14.60        48.79        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       19.36         7.00        13.15         0.13         0.00         0.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       13.22         0.20        11.57         6.31         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        5.13         4.31         4.34         5.13         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        9.90        11.15        38.63         8.55         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       11.31        49.22        23.90        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       34.92        19.43        16.01        35.54        33.83         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        1.15        13.02        34.98         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      111.78       111.91        25.08        26.99        29.65        27.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JH 
       13.81        12.72         3.22        21.60        21.60        13.94 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       33.60        18.61        38.40         5.72        76.41         3.78 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84        34.68         9.57        17.72        78.44        11.80 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        1.51        13.08         9.04         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
        4.90         6.71        64.47         3.45        11.01        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
        7.33         3.39         8.22        30.87        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       27.39         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 
        0.99         0.16         0.43         9.90         7.23        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        84.72        16.24        15.42        12.16        14.70 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        11.05         5.79 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                       111.09                        124.31 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        15.95                         13.81 
[1] "0.1 - 111.1 (15.9)" "0.0 - 124.3 (13.8)"
[1] "hr=" "1.1"
D29V2, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q34.3) MUTATED   43 35
  DEL PEAK  6(4Q34.3) WILD-TYPE 99 99
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           78                           198 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           35                            99 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JN 
       16.57       112.04        28.08       115.53        11.87        56.19 
TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F 
       66.08        46.98        86.93       103.59        21.47        43.69 
TCGA-D3-A51N TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW 
       10.03       151.53        54.67         9.90        66.25        36.03 
TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5UL 
      117.21        61.18       215.44        15.68        10.16         3.55 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29C 
       27.22        94.98        33.73       109.64       168.26        47.84 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 
       44.35       345.96       171.55        17.92        39.29        58.75 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GU TCGA-EE-A2M5 
      208.04        48.72        75.48       101.95        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AG TCGA-EE-A3J4 
      129.27       167.90        43.23        41.59        23.47       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 
       34.32        53.19        27.35        33.40        31.40        13.94 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG 
       98.40        12.59        13.02        37.25        23.34        31.27 
TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1Z0 
       32.05        80.32        46.98        15.16         7.00       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       28.08        27.72       357.37        40.27        15.45         9.70 
TCGA-FS-A1ZJ TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A266 TCGA-GN-A4U9 
       47.38         0.20        47.54        14.04        10.13        12.62 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.67       112.57        71.80       133.25        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        48.76       113.52        42.08        12.10       171.58 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       45.11       130.72        58.06        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H 
       24.53        13.87         9.34        39.75       161.85        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      131.90        18.38        51.68        15.06       110.93       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX 
      137.92       166.19         7.43       125.19         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I0 
       11.34         3.25        25.18        22.95        48.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
      194.83       176.55        35.93       107.34        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH 
       23.44        68.09        28.60        10.49        13.87        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       45.11        35.01        52.01         6.35        12.20        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        14.70        26.89        68.15         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       78.87        13.55        63.35        80.61        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         2.60        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        55.92        25.87        46.82       102.90        24.43 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       47.54        67.43       314.56       135.95        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        90.97        13.91        14.30        55.59        44.88 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
       16.96       204.66        96.23       144.76       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65       103.56       136.47        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        54.51        13.81       138.81       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       36.95        64.08       101.79       148.08        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        9.17        77.75        48.89        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
      148.18        79.99        43.82        20.15        16.37       247.04 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YW 
       33.21        92.98       174.21         4.90       210.08       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
       48.59       228.59        20.91         7.79        48.85        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        49.45        77.88        22.92         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         7.23       120.46       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        32.48        39.58        46.36       294.77         6.67 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         0.20                          0.16 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                       357.37                        314.56 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        42.41                         49.81 
[1] "0.2 - 357.4 (42.4)" "0.2 - 314.6 (49.8)"
[1] "hr=" "1"  
D29V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  6(4Q34.3) MUTATED                   12             2
  DEL PEAK  6(4Q34.3) WILD-TYPE                 25             2
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  6(4Q34.3) MUTATED                                          20
  DEL PEAK  6(4Q34.3) WILD-TYPE                                        40
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  6(4Q34.3) MUTATED                    43
  DEL PEAK  6(4Q34.3) WILD-TYPE                 136
D29V4, multiclass
                                           clus
vv                                          DEL PEAK  6(4Q34.3) MUTATED
  DISTANT METASTASIS                                                 12
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          20
  REGIONAL LYMPH NODE                                                43
                                           clus
vv                                          DEL PEAK  6(4Q34.3) WILD-TYPE
  DISTANT METASTASIS                                                   25
  PRIMARY TUMOR                                                         2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            40
  REGIONAL LYMPH NODE                                                 136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  6(4Q34.3) MUTATED             1       1       7        4        8
  DEL PEAK  6(4Q34.3) WILD-TYPE           9       5      16        6       17
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  6(4Q34.3) MUTATED          4         0         2         4
  DEL PEAK  6(4Q34.3) WILD-TYPE       13        10        12         6
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  6(4Q34.3) MUTATED           8          6          9         14
  DEL PEAK  6(4Q34.3) WILD-TYPE        24          8         14         34
                               vv
clus                            STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED          3
  DEL PEAK  6(4Q34.3) WILD-TYPE        9
D29V5, multiclass
             clus
vv            DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  I OR II NOS                           1                             9
  STAGE 0                               1                             5
  STAGE I                               7                            16
  STAGE IA                              4                             6
  STAGE IB                              8                            17
  STAGE II                              4                            13
  STAGE IIA                             0                            10
  STAGE IIB                             2                            12
  STAGE IIC                             4                             6
  STAGE III                             8                            24
  STAGE IIIA                            6                             8
  STAGE IIIB                            9                            14
  STAGE IIIC                           14                            34
  STAGE IV                              3                             9
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  6(4Q34.3) MUTATED      17 19 14 14
  DEL PEAK  6(4Q34.3) WILD-TYPE    36 41 41 43
D29V6, multiclass
       clus
vv      DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  T0+T1                          17                            36
  T2                             19                            41
  T3                             14                            41
  T4                             14                            43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  6(4Q34.3) MUTATED    34  17   9  13
  DEL PEAK  6(4Q34.3) WILD-TYPE 107  34  23  24
D29V7, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  N0                          34                           107
  N1                          17                            34
  N2                           9                            23
  N3                          13                            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  DEL PEAK  6(4Q34.3) MUTATED    71   1   0   2   1
  DEL PEAK  6(4Q34.3) WILD-TYPE 181   3   2   0   4
D29V8, multiclass
     clus
vv    DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  M0                           71                           181
  M1                            1                             3
  M1A                           0                             2
  M1B                           2                             0
  M1C                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   31 20
  DEL PEAK  6(4Q34.3) WILD-TYPE 73 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     31   20
  DEL PEAK  6(4Q34.3) WILD-TYPE   73   52
     clus
vv    DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  NO                           31                            73
  YES                          20                            52
[1] 2 2
[1] FALSE
D29V10, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q34.3) MUTATED    12  66
  DEL PEAK  6(4Q34.3) WILD-TYPE  22 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     12   66
  DEL PEAK  6(4Q34.3) WILD-TYPE   22  181
     clus
vv    DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  NO                           12                            22
  YES                          66                           181
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q34.3) MUTATED    38  40
  DEL PEAK  6(4Q34.3) WILD-TYPE  70 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     38   40
  DEL PEAK  6(4Q34.3) WILD-TYPE   70  133
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                          38                            70
  MALE                            40                           133
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q34.3) MUTATED       2                         0    76
  DEL PEAK  6(4Q34.3) WILD-TYPE     3                         1   199
D29V13, multiclass
                           clus
vv                          DEL PEAK  6(4Q34.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              76
                           clus
vv                          DEL PEAK  6(4Q34.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q34.3) MUTATED     0  77
  DEL PEAK  6(4Q34.3) WILD-TYPE   3 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      0   77
  DEL PEAK  6(4Q34.3) WILD-TYPE    3  197
                        clus
vv                       DEL PEAK  6(4Q34.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       DEL PEAK  6(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           197
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  7(5P15.31) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(5P15.31) MUTATED    28  29
  DEL PEAK  7(5P15.31) WILD-TYPE 109 104
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                            57                            213 
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                            29                            104 
$`DEL PEAK  7(5P15.31) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CC 
        8.52        68.22        11.41         7.50        92.42        61.38 
TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 
       24.00         5.39        47.87        48.79        35.80        17.56 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 TCGA-EE-A185 
       13.15         0.20        11.57        10.55         5.13         4.31 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 TCGA-EE-A2GB 
        1.18        37.97        12.03         8.09        23.90        39.39 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2MM 
       17.98        34.92        47.21        30.08         1.15        56.02 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 
       21.60         5.56        21.60        21.60        22.22         5.72 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZM 
        1.87         1.51        12.62         4.90         8.22        47.38 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4FB 
       40.64        27.39         0.82         3.22        14.20         5.98 
TCGA-FW-A3I3 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        0.20        12.85        24.85        31.33        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26D TCGA-OD-A75X 
       15.42        14.70        11.05 

$`DEL PEAK  7(5P15.31) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       21.14        88.50        69.90        30.87        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        45.11       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32        82.29        13.32         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
        8.84        20.48        13.94        95.38        52.01         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       13.22        14.60        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5SG 
        6.64        19.36         7.00        14.83         0.13         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        0.00        13.22         0.20         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        1.35        12.20        36.07         4.34         5.13         9.21 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        11.15        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        1.08        27.12         9.50         8.84         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        2.43         8.68         8.09        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
        8.94        34.29        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83        30.84         5.42        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      111.91        25.08        26.99        29.65        27.16        23.05 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD 
       15.95        12.72         3.22        22.92        16.14        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       38.40        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       11.80        13.08        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
        1.71        18.41        85.74         6.71         3.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         7.30         3.39        20.38        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.92        12.89        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.81        49.15         8.68         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       28.73        10.78         6.41         2.27         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A26A 
        0.16         0.43         9.90         7.23        84.72        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       11.84        10.65         5.79 

  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                         92.42                         124.31 
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                         14.20                          13.94 
[1] "0.2 - 92.4 (14.2)"  "0.0 - 124.3 (13.9)"
[1] "hr=" "1.2"
D30V2, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(5P15.31) MUTATED    29  29
  DEL PEAK  7(5P15.31) WILD-TYPE 113 105
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                            58                            218 
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                            29                            105 
$`DEL PEAK  7(5P15.31) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CC 
       16.67       168.00        11.87       113.52       171.58        86.93 
TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 
       24.53        21.47       137.92        48.89        36.03       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 
       13.87        10.16         3.55        29.82        27.22        68.15 
TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A2 
        4.96        13.55        47.84        56.42        37.35        24.43 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GR 
       47.54       314.56       135.95       208.04        48.72        14.30 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
      167.90        43.23        53.26        36.95        64.08        53.19 
TCGA-ER-A199 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A69P TCGA-FS-A1ZD 
        9.17        23.34        20.15        31.27         4.90        53.52 
TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F8 
      101.26        53.16        49.48        27.09        50.14       174.84 
TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
       26.73         0.20        14.04       120.46       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-OD-A75X 
       64.44        62.79        39.58       294.77 

$`DEL PEAK  7(5P15.31) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       115.53        69.90        48.76        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        45.11       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32       166.52        60.23        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       10.03        51.68        15.06       110.93       135.75       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       11.34         3.25         9.90        25.18        66.25        22.95 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       10.49        15.68        17.85        45.11        35.01        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        6.35        12.20         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       26.89       109.64       151.27        78.87       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       44.35        18.61        14.47        55.92       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      171.55        17.92        46.82       102.90        39.29        58.75 
TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       67.43        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        13.91        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       47.54       248.65       103.56       136.47        41.59       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
      138.81       172.18       127.20        34.32        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.37        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       92.98       174.21       210.08        15.16         7.00       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
      148.80        26.56        27.02        77.82        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       12.43        49.45        77.88        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U8 
        2.40         9.90         7.23        84.72        32.48        46.36 
TCGA-GN-A4U9 TCGA-QB-A6FS 
       12.62         6.67 

  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                          0.20                           0.16 
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                        314.56                         357.37 
  DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE 
                        47.690                         48.065 
[1] "0.2 - 314.6 (47.7)" "0.2 - 357.4 (48.1)"
[1] "hr=" "1.1"
D30V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  7(5P15.31) MUTATED                    9             0
  DEL PEAK  7(5P15.31) WILD-TYPE                 28             4
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  7(5P15.31) MUTATED                                          14
  DEL PEAK  7(5P15.31) WILD-TYPE                                        46
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK  7(5P15.31) MUTATED                    36
  DEL PEAK  7(5P15.31) WILD-TYPE                 143
D30V4, multiclass
                                           clus
vv                                          DEL PEAK  7(5P15.31) MUTATED
  DISTANT METASTASIS                                                   9
  PRIMARY TUMOR                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           14
  REGIONAL LYMPH NODE                                                 36
                                           clus
vv                                          DEL PEAK  7(5P15.31) WILD-TYPE
  DISTANT METASTASIS                                                    28
  PRIMARY TUMOR                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             46
  REGIONAL LYMPH NODE                                                  143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  7(5P15.31) MUTATED             2       2       5        3        3
  DEL PEAK  7(5P15.31) WILD-TYPE           8       4      18        7       22
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  7(5P15.31) MUTATED          2         1         5         5
  DEL PEAK  7(5P15.31) WILD-TYPE       15         9         9         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  7(5P15.31) MUTATED           5          3          7         10
  DEL PEAK  7(5P15.31) WILD-TYPE        27         11         16         38
                                vv
clus                             STAGE IV
  DEL PEAK  7(5P15.31) MUTATED          2
  DEL PEAK  7(5P15.31) WILD-TYPE       10
D30V5, multiclass
             clus
vv            DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE
  I OR II NOS                            2                              8
  STAGE 0                                2                              4
  STAGE I                                5                             18
  STAGE IA                               3                              7
  STAGE IB                               3                             22
  STAGE II                               2                             15
  STAGE IIA                              1                              9
  STAGE IIB                              5                              9
  STAGE IIC                              5                              5
  STAGE III                              5                             27
  STAGE IIIA                             3                             11
  STAGE IIIB                             7                             16
  STAGE IIIC                            10                             38
  STAGE IV                               2                             10
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK  7(5P15.31) MUTATED       8 15  7 17
  DEL PEAK  7(5P15.31) WILD-TYPE    45 45 48 40
D30V6, multiclass
       clus
vv      DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE
  T0+T1                            8                             45
  T2                              15                             45
  T3                               7                             48
  T4                              17                             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK  7(5P15.31) MUTATED    29  12   5   8
  DEL PEAK  7(5P15.31) WILD-TYPE 112  39  27  29
D30V7, multiclass
    clus
vv   DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE
  N0                           29                            112
  N1                           12                             39
  N2                            5                             27
  N3                            8                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK  7(5P15.31) MUTATED    52   1   0   0   1
  DEL PEAK  7(5P15.31) WILD-TYPE 200   3   2   2   4
D30V8, multiclass
     clus
vv    DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE
  M0                            52                            200
  M1                             1                              3
  M1A                            0                              2
  M1B                            0                              2
  M1C                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                                cls
clus                              0  1
  DEL PEAK  7(5P15.31) MUTATED   15 23
  DEL PEAK  7(5P15.31) WILD-TYPE 89 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.31) MUTATED     15   23
  DEL PEAK  7(5P15.31) WILD-TYPE   89   49
     clus
vv    DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE
  NO                            15                             89
  YES                           23                             49
[1] 2 2
[1] FALSE
D30V10, binary
                                cls
clus                               0   1
  DEL PEAK  7(5P15.31) MUTATED     4  55
  DEL PEAK  7(5P15.31) WILD-TYPE  30 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.31) MUTATED      4   55
  DEL PEAK  7(5P15.31) WILD-TYPE   30  192
     clus
vv    DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE
  NO                             4                             30
  YES                           55                            192
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, binary
                                cls
clus                               0   1
  DEL PEAK  7(5P15.31) MUTATED    27  32
  DEL PEAK  7(5P15.31) WILD-TYPE  81 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.31) MUTATED     27   32
  DEL PEAK  7(5P15.31) WILD-TYPE   81  141
        clus
vv       DEL PEAK  7(5P15.31) MUTATED DEL PEAK  7(5P15.31) WILD-TYPE
  FEMALE                           27                             81
  MALE                             32                            141
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(5P15.31) MUTATED       3                         1    55
  DEL PEAK  7(5P15.31) WILD-TYPE     2                         0   220
D30V13, multiclass
                           clus
vv                          DEL PEAK  7(5P15.31) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               55
                           clus
vv                          DEL PEAK  7(5P15.31) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                                cls
clus                               0   1
  DEL PEAK  7(5P15.31) MUTATED     0  57
  DEL PEAK  7(5P15.31) WILD-TYPE   3 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.31) MUTATED      0   57
  DEL PEAK  7(5P15.31) WILD-TYPE    3  217
                        clus
vv                       DEL PEAK  7(5P15.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK  7(5P15.31) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            217
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  8(5Q11.2) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(5Q11.2) MUTATED    37  34
  DEL PEAK  8(5Q11.2) WILD-TYPE 100  99
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           71                           199 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           34                            99 
$`DEL PEAK  8(5Q11.2) MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       28.08        22.55        11.41         6.31        92.42        64.44 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       15.25        61.38         5.39        95.38        52.01        47.87 
TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 
        4.01        13.22        48.79        35.80        10.03        44.52 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20H 
       36.69        17.56        11.57        10.55         4.31         9.21 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29V 
       37.97        11.15        38.63        27.12        12.03         2.43 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       23.90        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP 
       30.08        28.31         1.15        63.42        56.02        26.99 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 
      122.73         3.68        30.15        12.72        21.60        21.60 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH 
        5.72        25.18        34.88         1.87         1.51        11.74 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       85.74         4.90         3.45        12.89         8.65        40.64 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 
       27.39         0.82         3.22        14.20         5.98        12.85 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-OD-A75X 
       24.85        10.13        16.24        15.42        11.05 

$`DEL PEAK  8(5Q11.2) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        69.90        30.87         7.50        36.16 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        45.11       114.67        46.98        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       20.48        13.94         1.55         6.97        23.11         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        11.31        14.60        51.12        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
        7.00        14.83        13.15         0.20         0.13         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        0.00        13.22         0.20         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
        1.35        12.20         5.13        36.07         4.34         5.13 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        1.18         7.99         9.90         8.55         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
        9.50         8.09         8.84         9.99         6.48         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GJ 
        8.09        11.31        49.22         9.67         8.94        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       16.01        35.54        33.83        30.84         5.42        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      111.78       111.91        25.08        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
       23.05         5.56       124.31        25.84        13.81        15.95 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
        3.22        22.92        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       76.41         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG 
       36.07        17.72        78.44        11.80        13.08        12.62 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 
        9.04         6.58        22.49         1.71        18.41         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.58         5.36        64.47        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       19.53        11.08         7.17        30.87        12.92        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       52.08         8.81        49.15         8.68         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
        7.36        28.73        10.78         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       31.33        84.72        12.16        14.70        11.84        10.65 
TCGA-QB-A6FS 
        5.79 

  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                         0.82                          0.00 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                       122.73                        124.31 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                        17.98                         13.32 
[1] "0.8 - 122.7 (18.0)" "0.0 - 124.3 (13.3)"
[1] "hr=" "1.2"
D31V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(5Q11.2) MUTATED    39  35
  DEL PEAK  8(5Q11.2) WILD-TYPE 103  99
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           74                           202 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           35                            99 
$`DEL PEAK  8(5Q11.2) MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       28.08        31.59        11.87        12.10       171.58        66.08 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       58.06        86.93        21.47       110.93       135.75       137.92 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
      151.53         6.41        11.34        66.25        48.89        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EE-A17X 
       20.38       107.34        61.18       215.44         3.55        29.82 
TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       27.22         4.96       168.26        47.84        13.97        39.62 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC 
       44.35        56.42        25.87        24.43        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GR 
      314.56       135.95       208.04        48.72        75.48        14.30 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       96.23       167.90       248.65       122.73         3.68        54.51 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19H 
      138.81        36.95        64.08         9.17        98.40       152.35 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX 
       23.34        20.15        32.05       174.21         4.90        48.59 
TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 
       23.93       133.55        53.16        49.48        27.09        50.14 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 
      174.84        26.73        14.04       120.46        10.13        64.44 
TCGA-GN-A268 TCGA-OD-A75X 
       62.79       294.77 

$`DEL PEAK  8(5Q11.2) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        69.90        48.76       113.52        42.08 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        45.11       130.72        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 
       51.68        15.06       166.19         7.43       125.19        54.67 
TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY 
        3.65         3.25         9.90        25.18        22.95       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      194.83       176.55        35.93        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        28.60        10.49        15.68        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       17.85        45.11        35.01        52.01         6.35        12.20 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64       151.27        78.87        13.55        63.35        80.61 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        32.19         2.60        18.61        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92       345.96       171.55        17.92        46.82       102.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       39.29        58.75        89.33        54.74        79.66        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        13.91        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
      103.20        16.96       204.66       144.76       203.05        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       25.84        13.81        23.47       172.18       127.20        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       35.44        13.94        50.76        77.75        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       268.93         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       43.82        16.37        31.27       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       33.21        92.98       210.08        15.16         7.00       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
       26.56        27.02        77.82        66.67        28.73        12.43 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A 
        2.40         9.90         7.23       117.93        84.72        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       39.58        46.36        12.62         6.67 

  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                         3.55                          0.16 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                       314.56                        357.37 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                        49.81                         46.98 
[1] "3.5 - 314.6 (49.8)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.2"
D31V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  8(5Q11.2) MUTATED                   12             1
  DEL PEAK  8(5Q11.2) WILD-TYPE                 25             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  8(5Q11.2) MUTATED                                          18
  DEL PEAK  8(5Q11.2) WILD-TYPE                                        42
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  8(5Q11.2) MUTATED                    46
  DEL PEAK  8(5Q11.2) WILD-TYPE                 133
D31V4, multiclass
                                           clus
vv                                          DEL PEAK  8(5Q11.2) MUTATED
  DISTANT METASTASIS                                                 12
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          18
  REGIONAL LYMPH NODE                                                46
                                           clus
vv                                          DEL PEAK  8(5Q11.2) WILD-TYPE
  DISTANT METASTASIS                                                   25
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            42
  REGIONAL LYMPH NODE                                                 133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  8(5Q11.2) MUTATED             4       2       9        3        4
  DEL PEAK  8(5Q11.2) WILD-TYPE           6       4      14        7       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  8(5Q11.2) MUTATED          5         0         5         4
  DEL PEAK  8(5Q11.2) WILD-TYPE       12        10         9         6
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  8(5Q11.2) MUTATED           7          2          9         13
  DEL PEAK  8(5Q11.2) WILD-TYPE        25         12         14         35
                               vv
clus                            STAGE IV
  DEL PEAK  8(5Q11.2) MUTATED          3
  DEL PEAK  8(5Q11.2) WILD-TYPE        9
D31V5, multiclass
             clus
vv            DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE
  I OR II NOS                           4                             6
  STAGE 0                               2                             4
  STAGE I                               9                            14
  STAGE IA                              3                             7
  STAGE IB                              4                            21
  STAGE II                              5                            12
  STAGE IIA                             0                            10
  STAGE IIB                             5                             9
  STAGE IIC                             4                             6
  STAGE III                             7                            25
  STAGE IIIA                            2                            12
  STAGE IIIB                            9                            14
  STAGE IIIC                           13                            35
  STAGE IV                              3                             9
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  8(5Q11.2) MUTATED      14 18 10 20
  DEL PEAK  8(5Q11.2) WILD-TYPE    39 42 45 37
D31V6, multiclass
       clus
vv      DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE
  T0+T1                          14                            39
  T2                             18                            42
  T3                             10                            45
  T4                             20                            37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  8(5Q11.2) MUTATED    39  16   6  11
  DEL PEAK  8(5Q11.2) WILD-TYPE 102  35  26  26
D31V7, multiclass
    clus
vv   DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE
  N0                          39                           102
  N1                          16                            35
  N2                           6                            26
  N3                          11                            26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  DEL PEAK  8(5Q11.2) MUTATED    70   0   1   2   1
  DEL PEAK  8(5Q11.2) WILD-TYPE 182   4   1   0   4
D31V8, multiclass
     clus
vv    DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE
  M0                           70                           182
  M1                            0                             4
  M1A                           1                             1
  M1B                           2                             0
  M1C                           1                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                               cls
clus                             0  1
  DEL PEAK  8(5Q11.2) MUTATED   23 23
  DEL PEAK  8(5Q11.2) WILD-TYPE 81 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q11.2) MUTATED     23   23
  DEL PEAK  8(5Q11.2) WILD-TYPE   81   49
     clus
vv    DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE
  NO                           23                            81
  YES                          23                            49
[1] 2 2
[1] FALSE
D31V10, binary
                               cls
clus                              0   1
  DEL PEAK  8(5Q11.2) MUTATED     7  70
  DEL PEAK  8(5Q11.2) WILD-TYPE  27 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q11.2) MUTATED      7   70
  DEL PEAK  8(5Q11.2) WILD-TYPE   27  177
     clus
vv    DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE
  NO                            7                            27
  YES                          70                           177
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, binary
                               cls
clus                              0   1
  DEL PEAK  8(5Q11.2) MUTATED    30  47
  DEL PEAK  8(5Q11.2) WILD-TYPE  78 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q11.2) MUTATED     30   47
  DEL PEAK  8(5Q11.2) WILD-TYPE   78  126
        clus
vv       DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE
  FEMALE                          30                            78
  MALE                            47                           126
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5Q11.2) MUTATED       1                         0    76
  DEL PEAK  8(5Q11.2) WILD-TYPE     4                         1   199
D31V13, multiclass
                           clus
vv                          DEL PEAK  8(5Q11.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              76
                           clus
vv                          DEL PEAK  8(5Q11.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                               cls
clus                              0   1
  DEL PEAK  8(5Q11.2) MUTATED     0  75
  DEL PEAK  8(5Q11.2) WILD-TYPE   3 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q11.2) MUTATED      0   75
  DEL PEAK  8(5Q11.2) WILD-TYPE    3  199
                        clus
vv                       DEL PEAK  8(5Q11.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          75
                        clus
vv                       DEL PEAK  8(5Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           199
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  9(5Q31.3) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(5Q31.3) MUTATED   49 51
  DEL PEAK  9(5Q31.3) WILD-TYPE 88 82
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                          100                           170 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                           51                            82 
$`DEL PEAK  9(5Q31.3) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
        8.52        28.08        22.55        11.41         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV 
       92.42        64.44        15.25        61.38        24.00         5.39 
TCGA-D3-A51N TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6E9 
        8.84        95.38        52.01        47.87         4.01         9.90 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 
       13.22        48.79        35.80        51.12        10.03        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17X 
       36.69        25.15        17.56         0.13         0.00        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A20I 
       10.55         6.31         8.12         4.31         9.21         1.18 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29S 
       37.97        38.63         8.55        27.12        12.03         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC 
        2.43         8.09        11.31        23.90        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       17.98        34.92        47.21        30.08        19.43        28.31 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MJ 
        1.15        34.98        98.27         2.70        44.25        63.42 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AD 
       56.02        26.99        21.60        29.65       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI 
       30.15        12.72        21.60        21.60        16.14        33.60 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND 
       18.61         5.72        25.18        34.88         9.57         1.87 
TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZB 
        1.51        11.74        85.74         4.90         3.45         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
       20.38        11.08        47.38         8.65        40.64        27.39 
TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 
       53.85        28.73        14.20         5.98        12.85        24.85 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-OD-A75X 
       10.13        16.24        15.42        11.05 

$`DEL PEAK  9(5Q31.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA 
       16.47       111.09        32.42        70.16       110.79        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP 
       68.22        69.90        30.87        36.16        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML 
      114.67        46.98        46.32        82.29        13.32         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        26.37        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
       41.10        17.72        20.48        13.94         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 
       23.11         2.89        11.31        14.60        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
        9.99         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
       14.83        13.15         0.20         0.00        13.22         0.20 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C 
        1.12         1.35        12.20         5.13        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
        5.13         7.99         9.90        11.15         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
        9.50         8.09         8.84         6.48         8.68        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
        9.67         8.94        16.01        35.54        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
        5.42        13.02        36.33         8.84         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
        9.53        29.46         7.96        14.56       111.78       111.91 
TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       25.08        27.16        23.05         5.56       124.31        25.84 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD 
       13.81        15.95         3.22        22.92        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
        0.46        13.94        31.40        12.95        38.40        76.41 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
        3.78         3.52        11.90        11.11       114.15         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W 
       13.45        28.60        42.84        34.68        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       78.44        11.80        13.08        12.62         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       22.49         1.71        18.41         6.71         3.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        7.30         8.22        19.53         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       12.89        52.08         8.81        49.15         8.68         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
        5.23         3.22         7.36        10.78         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
        7.23        31.33        84.72        12.16        14.70        11.84 
TCGA-GN-A4U9 TCGA-QB-A6FS 
       10.65         5.79 

  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                            0                             0 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                       122.73                        124.31 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                       18.295                        13.185 
[1] "0.0 - 122.7 (18.3)" "0.0 - 124.3 (13.2)"
[1] "hr=" "1"  
D32V2, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(5Q31.3) MUTATED   51 52
  DEL PEAK  9(5Q31.3) WILD-TYPE 91 82
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                          103                           173 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                           52                            82 
$`DEL PEAK  9(5Q31.3) MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       16.67        28.08        31.59        11.87       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV 
      171.58        66.08        58.06        86.93        24.53        21.47 
TCGA-D3-A51N TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A1JX 
       10.03       110.93       135.75       137.92       151.53         6.41 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       11.34         9.90        66.25        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A5KH 
       20.38       107.34        61.18        53.92       215.44        17.85 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       35.01         3.55        29.82        27.22         8.65        94.98 
TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        4.96       168.26        13.55        47.84        39.62        72.07 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       44.35        56.42        55.92        25.87        17.92        46.82 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       24.43        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M6 
       48.72        89.33        75.48        14.30        44.88       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
       28.83       103.20        96.23       167.90       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 
      103.56       122.73         3.68        54.51       138.81        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B 
       64.08        34.32       148.08        35.44         9.17        98.40 
TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A 
      152.35        50.89        23.34        20.15        32.05       174.21 
TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZM 
        4.90        48.59        48.85       357.37        15.45       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 
      133.55        53.16        49.48        77.82        28.73       174.84 
TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       26.73        14.04       120.46        10.13        64.44        62.79 
TCGA-OD-A75X 
      294.77 

$`DEL PEAK  9(5Q31.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA 
       16.57       112.04       112.57        71.80       133.25        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP 
      168.00        69.90        48.76        42.08        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML 
      130.72        46.98        46.32       166.52        60.23        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        39.75       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
      131.90        18.38        51.68        15.06       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG 
      125.19        54.67         3.65         3.25        25.18        22.95 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      194.83       176.55        35.93        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       28.60        10.49        15.68        13.87        10.16        45.11 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       52.01         6.35        12.20        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B 
       68.15       109.64       151.27        78.87        63.35        80.61 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       13.97        32.19         2.60        18.61        37.35        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GK 
      345.96       171.55       102.90        39.29        58.75        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       79.66        90.97       101.95        13.91        55.59        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH 
       21.67        19.76        61.51        47.28       103.27        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT 
      204.66       144.76       203.05        47.54       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       53.26       124.31        25.84        13.81        23.47       172.18 
TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
      127.20        53.19        27.35        33.40       101.79        31.40 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       13.94        50.76        77.75        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
      162.08        37.25       148.18        79.99        43.82        16.37 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       31.27       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      210.08        15.16         7.00       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE 
       20.91        28.08         7.79        27.72        53.52        40.27 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
        9.70        32.75        47.38        23.93        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 
      148.80        26.56        27.09        27.02        50.14        66.67 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
        0.16         2.40         9.90         7.23       117.93        84.72 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       32.48        39.58        46.36        12.62         6.67 

  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                         3.55                          0.16 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                       357.37                        345.96 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                        49.48                         46.98 
[1] "3.5 - 357.4 (49.5)" "0.2 - 346.0 (47.0)"
[1] "hr=" "1.1"
D32V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  9(5Q31.3) MUTATED                   14             2
  DEL PEAK  9(5Q31.3) WILD-TYPE                 23             2
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  9(5Q31.3) MUTATED                                          24
  DEL PEAK  9(5Q31.3) WILD-TYPE                                        36
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  9(5Q31.3) MUTATED                    66
  DEL PEAK  9(5Q31.3) WILD-TYPE                 113
D32V4, multiclass
                                           clus
vv                                          DEL PEAK  9(5Q31.3) MUTATED
  DISTANT METASTASIS                                                 14
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          24
  REGIONAL LYMPH NODE                                                66
                                           clus
vv                                          DEL PEAK  9(5Q31.3) WILD-TYPE
  DISTANT METASTASIS                                                   23
  PRIMARY TUMOR                                                         2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            36
  REGIONAL LYMPH NODE                                                 113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK  9(5Q31.3) MUTATED             5       2      13        4        6
  DEL PEAK  9(5Q31.3) WILD-TYPE           5       4      10        6       19
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  9(5Q31.3) MUTATED          6         3         6         5
  DEL PEAK  9(5Q31.3) WILD-TYPE       11         7         8         5
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  9(5Q31.3) MUTATED          11          7          9         15
  DEL PEAK  9(5Q31.3) WILD-TYPE        21          7         14         33
                               vv
clus                            STAGE IV
  DEL PEAK  9(5Q31.3) MUTATED          5
  DEL PEAK  9(5Q31.3) WILD-TYPE        7
D32V5, multiclass
             clus
vv            DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE
  I OR II NOS                           5                             5
  STAGE 0                               2                             4
  STAGE I                              13                            10
  STAGE IA                              4                             6
  STAGE IB                              6                            19
  STAGE II                              6                            11
  STAGE IIA                             3                             7
  STAGE IIB                             6                             8
  STAGE IIC                             5                             5
  STAGE III                            11                            21
  STAGE IIIA                            7                             7
  STAGE IIIB                            9                            14
  STAGE IIIC                           15                            33
  STAGE IV                              5                             7
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  9(5Q31.3) MUTATED      18 25 16 28
  DEL PEAK  9(5Q31.3) WILD-TYPE    35 35 39 29
D32V6, multiclass
       clus
vv      DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE
  T0+T1                          18                            35
  T2                             25                            35
  T3                             16                            39
  T4                             28                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  9(5Q31.3) MUTATED   58 19  9 15
  DEL PEAK  9(5Q31.3) WILD-TYPE 83 32 23 22
D32V7, multiclass
    clus
vv   DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE
  N0                          58                            83
  N1                          19                            32
  N2                           9                            23
  N3                          15                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  DEL PEAK  9(5Q31.3) MUTATED    97   0   1   2   3
  DEL PEAK  9(5Q31.3) WILD-TYPE 155   4   1   0   2
D32V8, multiclass
     clus
vv    DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE
  M0                           97                           155
  M1                            0                             4
  M1A                           1                             1
  M1B                           2                             0
  M1C                           3                             2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q31.3) MUTATED   42 27
  DEL PEAK  9(5Q31.3) WILD-TYPE 62 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q31.3) MUTATED     42   27
  DEL PEAK  9(5Q31.3) WILD-TYPE   62   45
     clus
vv    DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE
  NO                           42                            62
  YES                          27                            45
[1] 2 2
[1] FALSE
D32V10, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q31.3) MUTATED     8  98
  DEL PEAK  9(5Q31.3) WILD-TYPE  26 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q31.3) MUTATED      8   98
  DEL PEAK  9(5Q31.3) WILD-TYPE   26  149
     clus
vv    DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE
  NO                            8                            26
  YES                          98                           149
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q31.3) MUTATED    42  64
  DEL PEAK  9(5Q31.3) WILD-TYPE  66 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q31.3) MUTATED     42   64
  DEL PEAK  9(5Q31.3) WILD-TYPE   66  109
        clus
vv       DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE
  FEMALE                          42                            66
  MALE                            64                           109
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q31.3) MUTATED       2                         0   104
  DEL PEAK  9(5Q31.3) WILD-TYPE     3                         1   171
D32V13, multiclass
                           clus
vv                          DEL PEAK  9(5Q31.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             104
                           clus
vv                          DEL PEAK  9(5Q31.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q31.3) MUTATED     0 104
  DEL PEAK  9(5Q31.3) WILD-TYPE   3 170
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q31.3) MUTATED      0  104
  DEL PEAK  9(5Q31.3) WILD-TYPE    3  170
                        clus
vv                       DEL PEAK  9(5Q31.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                         104
                        clus
vv                       DEL PEAK  9(5Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           170
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 10(6Q22.31) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(6Q22.31) MUTATED   79 82
  DEL PEAK 10(6Q22.31) WILD-TYPE 58 51
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                           161                            109 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            82                             51 
$`DEL PEAK 10(6Q22.31) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 
       16.47       111.09        32.42        22.55        10.29        85.32 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
       68.22        69.90        11.41        30.87        36.16        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3ML 
       56.19        64.44        45.11        15.25        24.00         6.31 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
      103.59        26.37         5.39        80.22        42.71        41.10 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z3 
        8.84        13.94        95.38        52.01         1.55         2.89 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       11.31        13.22        14.60        48.79        51.12        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 
        9.99        36.69        25.15         4.93         6.64         7.00 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
       17.56         0.00        13.22         0.20        10.55         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
        8.55         4.41         1.08        27.12         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        23.90         9.67         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
       34.92        35.54        33.83        30.84         5.42        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MH TCGA-EE-A2MK 
        8.84        98.27         2.70        47.51         7.96       111.78 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       26.99        27.16        23.05         5.56       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        3.68        13.81        15.95         3.22        22.92        21.60 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B 
       22.22        13.94        33.60        18.61         5.72        25.18 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       42.84        34.68         9.57         1.51        13.08        12.62 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW 
        6.58        22.49         1.71         4.90         3.58        64.47 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
        3.45        23.80         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       11.08         7.17        30.87        12.92        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
        8.81        49.15        40.64         8.68        27.39         5.23 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 
        3.22         7.36        28.73        14.20         5.98         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        0.99         0.13         7.23        31.33        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        11.84        10.65        11.05         5.79 

$`DEL PEAK 10(6Q22.31) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
        8.52        70.16       110.79        28.08        45.83        81.24 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ 
        8.38        21.14        88.50         7.50         6.31       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       46.98        46.32        82.29        61.38        13.32         9.34 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       15.09        17.72        20.48        47.87         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 
        4.01         9.90        35.80        10.03        13.68        44.52 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       22.36        19.36        14.83        13.15         0.20         0.13 
TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29E 
        0.00        11.57         6.31         4.34         5.13        38.63 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
        9.50        12.03        34.29        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 
       16.01        28.31         1.15        13.02        34.98         6.18 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
        9.53        29.46        44.25        14.56        63.42       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AE 
       56.02        25.08        21.60        29.65       124.31        30.15 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 
       12.72        21.60        16.14        27.35         0.46        31.40 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M 
       12.95        38.40        76.41         3.78        13.45        28.60 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NH 
       36.07        17.72        78.44        11.80         1.87        11.74 
TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YY 
        9.04        18.41        85.74         6.71         5.36        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP 
       14.24        15.52         7.33        19.53        12.89        52.08 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV 
        0.82        53.85        10.78         6.41         2.27         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        0.43         9.90        12.85        24.85        84.72        10.13 
TCGA-GN-A26D 
       14.70 

  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                             0                              0 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                         12.92                          16.01 
[1] "0.0 - 122.7 (12.9)" "0.0 - 124.3 (16.0)"
[1] "hr=" "1.2"
D33V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(6Q22.31) MUTATED   83 83
  DEL PEAK 10(6Q22.31) WILD-TYPE 59 51
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                           166                            110 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            83                             51 
$`DEL PEAK 10(6Q22.31) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 
       16.57       112.04       112.57        31.59        43.43       103.10 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
      168.00        69.90        11.87        48.76        42.08       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3ML 
       56.19        66.08        45.11        58.06        24.53        13.87 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
      103.59        39.75        21.47       161.85        43.69       131.90 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A148 
       10.03        15.06       110.93       135.75       166.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
       54.67         3.65         6.41         3.25        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 
       22.95        48.89       117.21       194.83        35.93        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A5SG 
       53.92        65.92        68.09        10.49       215.44        45.11 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
        3.55        52.01        12.20        27.22        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H 
       14.70        26.89        68.15         4.96       109.64       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        80.61        47.84        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       32.19         2.60        44.35        37.35        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      345.96        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        39.29        58.75        47.54       314.56       135.95 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 
       79.66        90.97       101.95        13.91        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
      129.27        28.83        61.51        16.96       144.76       248.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        41.59        53.26       122.73        25.84         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JA 
       13.81        23.47       172.18       127.20        64.08        53.19 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
      101.79       148.08        35.44         9.17        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N 
       13.02        26.37       268.93       152.35         6.44        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET 
      162.08        50.89        20.15        16.37        31.27        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX 
       46.98        33.21         4.90        15.16       216.92        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
      202.65        27.72        48.85       357.37        53.52        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        32.75        47.38       101.26       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F2 
      148.80        53.16        26.56        49.48        27.02        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 
       66.67        28.73       174.84        26.73         0.20        22.92 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       47.54         7.23       117.93        64.44        62.79        32.48 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

$`DEL PEAK 10(6Q22.31) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       16.67        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ 
       65.49        23.77       115.53       113.52        12.10       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
       46.98        46.32       166.52        86.93        60.23         9.34 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       40.14        18.38        51.68       137.92         7.43       125.19 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 
       11.34         9.90        36.03        20.38       176.55       107.34 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       23.44        28.60        15.68        13.87        10.16        17.85 
TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F 
       35.01         6.35        29.82         8.65       151.27        78.87 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI 
       39.62        18.61        56.42        67.43       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       89.33        54.74        75.48        14.30        55.59        44.88 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       19.76        47.28       103.27       103.20       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AA 
      203.05       167.90        47.54        43.23       103.56       124.31 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       54.51       138.81        36.95        34.32        27.35        33.40 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19L 
       31.40        13.94        50.76        77.75        48.89       131.51 
TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       61.05        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 
       32.05       247.04        92.98       174.21       210.08         7.00 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZK 
      228.59        20.91        28.08         7.79        40.27        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       74.73        27.09        77.82        12.43        49.45        77.88 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
        0.16         2.40         9.90        14.04       120.46        84.72 
TCGA-GN-A266 TCGA-GN-A26D 
       10.13        39.58 

  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                          0.20                           0.16 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                        357.37                         247.04 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                        48.215                         47.410 
[1] "0.2 - 357.4 (48.2)" "0.2 - 247.0 (47.4)"
[1] "hr=" "1"  
D33V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 10(6Q22.31) MUTATED                   25             3
  DEL PEAK 10(6Q22.31) WILD-TYPE                 12             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 10(6Q22.31) MUTATED                                          40
  DEL PEAK 10(6Q22.31) WILD-TYPE                                        20
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 10(6Q22.31) MUTATED                   101
  DEL PEAK 10(6Q22.31) WILD-TYPE                  78
D33V4, multiclass
                                           clus
vv                                          DEL PEAK 10(6Q22.31) MUTATED
  DISTANT METASTASIS                                                  25
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           40
  REGIONAL LYMPH NODE                                                101
                                           clus
vv                                          DEL PEAK 10(6Q22.31) WILD-TYPE
  DISTANT METASTASIS                                                    12
  PRIMARY TUMOR                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             20
  REGIONAL LYMPH NODE                                                   78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 10(6Q22.31) MUTATED             7       4      12        6       17
  DEL PEAK 10(6Q22.31) WILD-TYPE           3       2      11        4        8
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 10(6Q22.31) MUTATED          9         6         6         4
  DEL PEAK 10(6Q22.31) WILD-TYPE        8         4         8         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 10(6Q22.31) MUTATED          18          9         14         32
  DEL PEAK 10(6Q22.31) WILD-TYPE        14          5          9         16
                                vv
clus                             STAGE IV
  DEL PEAK 10(6Q22.31) MUTATED          6
  DEL PEAK 10(6Q22.31) WILD-TYPE        6
D33V5, multiclass
             clus
vv            DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  I OR II NOS                            7                              3
  STAGE 0                                4                              2
  STAGE I                               12                             11
  STAGE IA                               6                              4
  STAGE IB                              17                              8
  STAGE II                               9                              8
  STAGE IIA                              6                              4
  STAGE IIB                              6                              8
  STAGE IIC                              4                              6
  STAGE III                             18                             14
  STAGE IIIA                             9                              5
  STAGE IIIB                            14                              9
  STAGE IIIC                            32                             16
  STAGE IV                               6                              6
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 10(6Q22.31) MUTATED      31 40 32 30
  DEL PEAK 10(6Q22.31) WILD-TYPE    22 20 23 27
D33V6, multiclass
       clus
vv      DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  T0+T1                           31                             22
  T2                              40                             20
  T3                              32                             23
  T4                              30                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 10(6Q22.31) MUTATED   84 32 20 23
  DEL PEAK 10(6Q22.31) WILD-TYPE 57 19 12 14
D33V7, multiclass
    clus
vv   DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  N0                           84                             57
  N1                           32                             19
  N2                           20                             12
  N3                           23                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 10(6Q22.31) MUTATED   155   2   1   1   3
  DEL PEAK 10(6Q22.31) WILD-TYPE  97   2   1   1   2
D33V8, multiclass
     clus
vv    DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  M0                           155                             97
  M1                             2                              2
  M1A                            1                              1
  M1B                            1                              1
  M1C                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.31) MUTATED   58 48
  DEL PEAK 10(6Q22.31) WILD-TYPE 46 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED     58   48
  DEL PEAK 10(6Q22.31) WILD-TYPE   46   24
     clus
vv    DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  NO                            58                             46
  YES                           48                             24
[1] 2 2
[1] FALSE
D33V10, binary
                                cls
clus                               0   1
  DEL PEAK 10(6Q22.31) MUTATED    22 147
  DEL PEAK 10(6Q22.31) WILD-TYPE  12 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED     22  147
  DEL PEAK 10(6Q22.31) WILD-TYPE   12  100
     clus
vv    DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  NO                            22                             12
  YES                          147                            100
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, binary
                                cls
clus                               0   1
  DEL PEAK 10(6Q22.31) MUTATED    68 101
  DEL PEAK 10(6Q22.31) WILD-TYPE  40  72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED     68  101
  DEL PEAK 10(6Q22.31) WILD-TYPE   40   72
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  FEMALE                           68                             40
  MALE                            101                             72
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q22.31) MUTATED       2                         1   166
  DEL PEAK 10(6Q22.31) WILD-TYPE     3                         0   109
D33V13, multiclass
                           clus
vv                          DEL PEAK 10(6Q22.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              166
                           clus
vv                          DEL PEAK 10(6Q22.31) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                                cls
clus                               0   1
  DEL PEAK 10(6Q22.31) MUTATED     1 165
  DEL PEAK 10(6Q22.31) WILD-TYPE   2 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED      1  165
  DEL PEAK 10(6Q22.31) WILD-TYPE    2  109
                        clus
vv                       DEL PEAK 10(6Q22.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          165
                        clus
vv                       DEL PEAK 10(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            109
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 11(6Q26) MUTATION ANALYSIS
D34V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 11(6Q26) MUTATED   81 85
  DEL PEAK 11(6Q26) WILD-TYPE 56 48
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        166                         104 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         85                          48 
$`DEL PEAK 11(6Q26) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 
       16.47       111.09        32.42        22.55        10.29        85.32 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
       68.22        69.90        11.41        30.87        36.16        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       56.19        64.44        45.11        15.25        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31       103.59        26.37         5.39        80.22        42.71 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       41.10        17.72         8.84        13.94        95.38        52.01 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        1.55        23.11         2.89        11.31        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 
       48.79        51.12        39.19         9.99        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN 
        4.93         6.64         7.00        17.56         0.00        13.22 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.31        36.07         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15         8.55         4.41         1.08        27.12 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        8.09         8.84         9.99         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       17.98        34.92        35.54        33.83        30.84         5.42 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       13.02        36.33         8.84        98.27         2.70        47.51 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
        7.96       111.78        26.99        27.16        23.05         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
      122.73        25.84         3.68        13.81        15.95         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       22.92        21.60        22.22        13.94        33.60        18.61 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       12.95         5.72        25.18         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      114.15        34.88         4.21        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       36.07        17.72         1.87         1.51        13.08        12.62 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX 
       22.49         1.71         4.90         3.58        64.47         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       23.80         7.30         3.39        20.38         8.22        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        30.87        12.92        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 
        3.22        28.73        14.20         5.98         0.20         0.99 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        0.13         7.23        31.33        16.24        15.42        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

$`DEL PEAK 11(6Q26) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
        8.52        70.16       110.79        28.08        45.83        81.24 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ 
        8.38        21.14        88.50         7.50         6.31       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51H 
       46.98        46.32        82.29        61.38         9.34        15.09 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1HW 
       20.48        47.87         6.97         4.01         9.90        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
       10.03        13.68        44.52        22.36        19.36        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17X 
       13.15         0.20         0.13         0.00         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P 
        6.31         4.34         5.13        38.63         9.50        12.03 
TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       11.31        34.29        47.21        30.08        19.43        16.01 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       28.31         1.15        34.98         6.18         9.53        29.46 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       44.25        14.56        63.42       111.91        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 
       21.60        29.65       124.31        30.15        12.72        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19A 
       16.14        27.35         0.46        31.40        38.40        76.41 
TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NH 
        3.78        13.45        28.60        78.44        11.80        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 
        9.04         6.58        18.41        85.74         6.71         5.36 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZK 
       11.01        14.24        15.52         7.33        19.53        12.89 
TCGA-FS-A1ZP TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       52.08        53.85         7.36        10.78         6.41         2.27 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
        0.16         0.43         9.90        12.85        24.85        84.72 
TCGA-GN-A266 TCGA-GN-A26D 
       10.13        14.70 

  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                          0                           0 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                     122.73                      124.31 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                     13.220                      15.305 
[1] "0.0 - 122.7 (13.2)" "0.0 - 124.3 (15.3)"
[1] "hr=" "1.2"
D34V2, survival
                             sevent
clus2                          0  1
  DEL PEAK 11(6Q26) MUTATED   85 86
  DEL PEAK 11(6Q26) WILD-TYPE 57 48
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        171                         105 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         86                          48 
$`DEL PEAK 11(6Q26) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 
       16.57       112.04       112.57        31.59        43.43       103.10 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
      168.00        69.90        11.87        48.76        42.08       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       56.19        66.08        45.11        58.06        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87       103.59        39.75        21.47       161.85        43.69 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      131.90        18.38        10.03        15.06       110.93       135.75 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
        3.25        25.18        66.25        22.95        48.89       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
      194.83        35.93        61.18        53.92        65.92        68.09 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y 
       10.49       215.44        45.11         3.55        52.01        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      109.64       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q 
       13.97        72.07        32.19         2.60        44.35        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        55.92       345.96        25.87       171.55        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      102.90        24.43        39.29        58.75        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
      135.95        79.66        90.97       101.95        13.91        55.59 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MH 
       94.82        21.67       129.27        28.83        61.51        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      144.76       248.65       136.47        41.59        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84         3.68        13.81        23.47       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       64.08        53.19       101.79       148.08        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        9.17        98.40        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      152.35         6.44        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3EV 
      148.18        23.34        20.15        16.37        31.27        46.98 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
       33.21         4.90        15.16       216.92        48.59       202.65 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        53.52        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 
       53.16        26.56        49.48        27.09        27.02        50.14 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       28.73       174.84        26.73         0.20        22.92        47.54 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
        7.23       117.93        64.44        62.79        32.48        46.36 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

$`DEL PEAK 11(6Q26) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       16.67        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ 
       65.49        23.77       115.53       113.52        12.10       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51H 
       46.98        46.32       166.52        86.93         9.34        40.14 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1HW 
       51.68       137.92         7.43        11.34         9.90        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 
       20.38       176.55       107.34        23.44        28.60        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        10.16        17.85        35.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29N 
       29.82         8.65       151.27        78.87        39.62        18.61 
TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       56.42        46.82        67.43       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD 
       54.74        75.48        14.30        44.88        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      103.27       103.20       204.66        96.23       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AH 
       47.54        43.23       103.56       124.31        54.51       138.81 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A198 
       36.95        34.32        27.35        33.40        31.40        50.76 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A1A1 TCGA-ER-A2NC 
       77.75        48.89       131.51        61.05        79.99        43.82 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
       32.05       247.04        80.32        92.98       174.21       210.08 
TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE 
        7.00       228.59        20.91        28.08         7.79        40.27 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FC 
       23.93        74.73        77.82        66.67        12.43        49.45 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       77.88         0.16         2.40         9.90        14.04       120.46 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D 
       84.72        10.13        39.58 

  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                       0.20                        0.16 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                     357.37                      247.04 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                      47.84                       47.54 
[1] "0.2 - 357.4 (47.8)" "0.2 - 247.0 (47.5)"
[1] "hr=" "1.1"
D34V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 11(6Q26) MUTATED                   27             3
  DEL PEAK 11(6Q26) WILD-TYPE                 10             1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 11(6Q26) MUTATED                                          39
  DEL PEAK 11(6Q26) WILD-TYPE                                        21
                             vv
clus                          REGIONAL LYMPH NODE
  DEL PEAK 11(6Q26) MUTATED                   104
  DEL PEAK 11(6Q26) WILD-TYPE                  75
D34V4, multiclass
                                           clus
vv                                          DEL PEAK 11(6Q26) MUTATED
  DISTANT METASTASIS                                               27
  PRIMARY TUMOR                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        39
  REGIONAL LYMPH NODE                                             104
                                           clus
vv                                          DEL PEAK 11(6Q26) WILD-TYPE
  DISTANT METASTASIS                                                 10
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          21
  REGIONAL LYMPH NODE                                                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 11(6Q26) MUTATED             7       4      12        6       19
  DEL PEAK 11(6Q26) WILD-TYPE           3       2      11        4        6
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 11(6Q26) MUTATED          9         4         7         4        19
  DEL PEAK 11(6Q26) WILD-TYPE        8         6         7         6        13
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 11(6Q26) MUTATED            8         16         32        6
  DEL PEAK 11(6Q26) WILD-TYPE          6          7         16        6
D34V5, multiclass
             clus
vv            DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  I OR II NOS                         7                           3
  STAGE 0                             4                           2
  STAGE I                            12                          11
  STAGE IA                            6                           4
  STAGE IB                           19                           6
  STAGE II                            9                           8
  STAGE IIA                           4                           6
  STAGE IIB                           7                           7
  STAGE IIC                           4                           6
  STAGE III                          19                          13
  STAGE IIIA                          8                           6
  STAGE IIIB                         16                           7
  STAGE IIIC                         32                          16
  STAGE IV                            6                           6
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 11(6Q26) MUTATED      34 40 31 31
  DEL PEAK 11(6Q26) WILD-TYPE    19 20 24 26
D34V6, multiclass
       clus
vv      DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  T0+T1                        34                          19
  T2                           40                          20
  T3                           31                          24
  T4                           31                          26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 11(6Q26) MUTATED   85 33 21 23
  DEL PEAK 11(6Q26) WILD-TYPE 56 18 11 14
D34V7, multiclass
    clus
vv   DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  N0                        85                          56
  N1                        33                          18
  N2                        21                          11
  N3                        23                          14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  DEL PEAK 11(6Q26) MUTATED   158   2   1   1   3
  DEL PEAK 11(6Q26) WILD-TYPE  94   2   1   1   2
D34V8, multiclass
     clus
vv    DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  M0                        158                          94
  M1                          2                           2
  M1A                         1                           1
  M1B                         1                           1
  M1C                         3                           2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                             cls
clus                           0  1
  DEL PEAK 11(6Q26) MUTATED   61 48
  DEL PEAK 11(6Q26) WILD-TYPE 43 24
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     61   48
  DEL PEAK 11(6Q26) WILD-TYPE   43   24
     clus
vv    DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  NO                         61                          43
  YES                        48                          24
[1] 2 2
[1] FALSE
D34V10, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q26) MUTATED    24 150
  DEL PEAK 11(6Q26) WILD-TYPE  10  97
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     24  150
  DEL PEAK 11(6Q26) WILD-TYPE   10   97
     clus
vv    DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  NO                         24                          10
  YES                       150                          97
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q26) MUTATED    72 102
  DEL PEAK 11(6Q26) WILD-TYPE  36  71
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     72  102
  DEL PEAK 11(6Q26) WILD-TYPE   36   71
        clus
vv       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  FEMALE                        72                          36
  MALE                         102                          71
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q26) MUTATED       1                         1   172
  DEL PEAK 11(6Q26) WILD-TYPE     4                         0   103
D34V13, multiclass
                           clus
vv                          DEL PEAK 11(6Q26) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                           172
                           clus
vv                          DEL PEAK 11(6Q26) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q26) MUTATED     2 170
  DEL PEAK 11(6Q26) WILD-TYPE   1 104
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED      2  170
  DEL PEAK 11(6Q26) WILD-TYPE    1  104
                        clus
vv                       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                           1
  NOT HISPANIC OR LATINO                       170                         104
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 12(8P23.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(8P23.3) MUTATED    29  34
  DEL PEAK 12(8P23.3) WILD-TYPE 108  99
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                           63                           207 
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                           34                            99 
$`DEL PEAK 12(8P23.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG 
       16.47        22.55        10.29        88.50        11.41         7.50 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MO TCGA-D3-A51N 
       92.42        64.44        15.25        46.98         9.34         8.84 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A6L9 TCGA-EE-A183 
       52.01         6.97         4.93         7.00         0.20        12.20 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V 
        4.34        37.97         4.41         1.08        27.12         2.43 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MG TCGA-EE-A2MH 
       23.90         9.67        30.08        13.02        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
       14.56        56.02        25.08        26.99        27.16         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 
      122.73        25.84        15.95         3.22        33.60        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19J TCGA-ER-A19S 
       38.40         5.72         3.78        11.90         4.21        36.07 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3PL TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA 
        1.87        13.08         1.71        11.01        23.80         7.30 
TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A264 
       20.38        12.92        40.64         2.27         0.99        31.33 
TCGA-GN-A265 TCGA-OD-A75X TCGA-QB-A6FS 
       84.72        11.05         5.79 

$`DEL PEAK 12(8P23.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       45.83        81.24        85.32         8.38        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP 
       69.90        30.87        36.16         6.31        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      114.67        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31       103.59        26.37         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       15.09        41.10        17.72        20.48        13.94        95.38 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       47.87         1.55        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       11.31        13.22        14.60        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       25.15        22.36         6.64        19.36        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       13.15         0.20         0.13         0.00         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31        36.07         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N 
        7.99         9.90        11.15        38.63         8.55         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         6.48         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
        8.09        11.31        49.22         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        47.21        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       28.31        33.83        30.84         5.42         1.15        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ 
        9.53        29.46        63.42       111.78       111.91        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       29.65        23.05       124.31         3.68        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
       27.35         0.46        13.94        31.40        18.61        76.41 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       25.18         3.52        11.11       114.15        34.88        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       28.60        42.84        34.68         9.57        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       11.80         1.51        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       22.49        18.41        85.74         4.90         6.71         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        5.36        64.47         3.45        14.24        15.52         7.33 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        3.39         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
        8.68        27.39         0.82         5.23        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       12.85        24.85        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       14.70        11.84        10.65 

  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                       122.73                        124.31 
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                        12.95                         14.60 
[1] "0.2 - 122.7 (12.9)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1.2"
D35V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(8P23.3) MUTATED    31  34
  DEL PEAK 12(8P23.3) WILD-TYPE 111 100
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                           65                           211 
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                           34                           100 
$`DEL PEAK 12(8P23.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG 
       16.57        31.59        43.43       115.53        11.87       113.52 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MO TCGA-D3-A51N 
      171.58        66.08        58.06        46.98         9.34        10.03 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-DA-A1IA TCGA-DA-A3F3 
      135.75         7.43       151.53         3.65        65.92        10.49 
TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L 
       12.20        26.89       151.27        47.84        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GS 
       44.35        25.87        24.43        39.29        48.72        55.59 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      103.20        16.96       204.66       167.90        47.54       248.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 
      136.47        53.26       122.73        25.84        23.47       172.18 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E 
      148.08        13.94        50.76         9.17        48.89        13.02 
TCGA-ER-A19J TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3PL TCGA-FS-A1YY 
        6.44        37.25        23.34        16.37        33.21       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A4FD 
      202.65        27.72       357.37        47.38        53.16        77.88 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-OD-A75X TCGA-QB-A6FS 
       22.92       117.93        84.72       294.77         6.67 

$`DEL PEAK 12(8P23.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        95.74       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP 
       69.90        48.76        42.08        12.10        56.19        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87       103.59        39.75        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       40.14       131.90        18.38        51.68        15.06       110.93 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 
      137.92       166.19       125.19        54.67         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        3.25         9.90        25.18        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        61.18        53.92        23.44        68.09        28.60 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y 
       35.01         3.55        52.01         6.35        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        14.70        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      109.64        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.97        39.62        72.07        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92       345.96       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        13.91        14.30        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
       96.23       144.76       203.05        43.23       103.56        41.59 
TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
      124.31         3.68        54.51        13.81       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
      101.79        31.40        35.44        77.75        98.40        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93       152.35       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      162.08        50.89       148.18        79.99        43.82        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       31.27        32.05       247.04        80.32        46.98        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      174.21         4.90       210.08        15.16         7.00       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
       48.59        20.91        28.08         7.79        48.85        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73       133.55        11.41       148.80        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU 
      174.84        12.43        26.73        49.45         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       10.13        64.44        62.79        32.48        39.58        46.36 
TCGA-GN-A4U9 
       12.62 

  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                         2.60                          0.16 
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                       357.37                        345.96 
  DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE 
                        47.38                         48.76 
[1] "2.6 - 357.4 (47.4)" "0.2 - 346.0 (48.8)"
[1] "hr=" "1"  
D35V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 12(8P23.3) MUTATED                   10             1
  DEL PEAK 12(8P23.3) WILD-TYPE                 27             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 12(8P23.3) MUTATED                                           9
  DEL PEAK 12(8P23.3) WILD-TYPE                                        51
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 12(8P23.3) MUTATED                    44
  DEL PEAK 12(8P23.3) WILD-TYPE                 135
D35V4, multiclass
                                           clus
vv                                          DEL PEAK 12(8P23.3) MUTATED
  DISTANT METASTASIS                                                 10
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           9
  REGIONAL LYMPH NODE                                                44
                                           clus
vv                                          DEL PEAK 12(8P23.3) WILD-TYPE
  DISTANT METASTASIS                                                   27
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            51
  REGIONAL LYMPH NODE                                                 135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 12(8P23.3) MUTATED             2       2       8        4        7
  DEL PEAK 12(8P23.3) WILD-TYPE           8       4      15        6       18
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 12(8P23.3) MUTATED          1         1         2         0
  DEL PEAK 12(8P23.3) WILD-TYPE       16         9        12        10
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 12(8P23.3) MUTATED           8          2          5         12
  DEL PEAK 12(8P23.3) WILD-TYPE        24         12         18         36
                               vv
clus                            STAGE IV
  DEL PEAK 12(8P23.3) MUTATED          4
  DEL PEAK 12(8P23.3) WILD-TYPE        8
D35V5, multiclass
             clus
vv            DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE
  I OR II NOS                           2                             8
  STAGE 0                               2                             4
  STAGE I                               8                            15
  STAGE IA                              4                             6
  STAGE IB                              7                            18
  STAGE II                              1                            16
  STAGE IIA                             1                             9
  STAGE IIB                             2                            12
  STAGE IIC                             0                            10
  STAGE III                             8                            24
  STAGE IIIA                            2                            12
  STAGE IIIB                            5                            18
  STAGE IIIC                           12                            36
  STAGE IV                              4                             8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 12(8P23.3) MUTATED      16 18  6 10
  DEL PEAK 12(8P23.3) WILD-TYPE    37 42 49 47
D35V6, multiclass
       clus
vv      DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE
  T0+T1                          16                            37
  T2                             18                            42
  T3                              6                            49
  T4                             10                            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 12(8P23.3) MUTATED    28  10   9  12
  DEL PEAK 12(8P23.3) WILD-TYPE 113  41  23  25
D35V7, multiclass
    clus
vv   DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE
  N0                          28                           113
  N1                          10                            41
  N2                           9                            23
  N3                          12                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  DEL PEAK 12(8P23.3) MUTATED    57   1   1   1   2
  DEL PEAK 12(8P23.3) WILD-TYPE 195   3   1   1   3
D35V8, multiclass
     clus
vv    DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE
  M0                           57                           195
  M1                            1                             3
  M1A                           1                             1
  M1B                           1                             1
  M1C                           2                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                               cls
clus                             0  1
  DEL PEAK 12(8P23.3) MUTATED   26 14
  DEL PEAK 12(8P23.3) WILD-TYPE 78 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.3) MUTATED     26   14
  DEL PEAK 12(8P23.3) WILD-TYPE   78   58
     clus
vv    DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE
  NO                           26                            78
  YES                          14                            58
[1] 2 2
[1] FALSE
D35V10, binary
                               cls
clus                              0   1
  DEL PEAK 12(8P23.3) MUTATED    10  55
  DEL PEAK 12(8P23.3) WILD-TYPE  24 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.3) MUTATED     10   55
  DEL PEAK 12(8P23.3) WILD-TYPE   24  192
     clus
vv    DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE
  NO                           10                            24
  YES                          55                           192
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, binary
                               cls
clus                              0   1
  DEL PEAK 12(8P23.3) MUTATED    23  42
  DEL PEAK 12(8P23.3) WILD-TYPE  85 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.3) MUTATED     23   42
  DEL PEAK 12(8P23.3) WILD-TYPE   85  131
        clus
vv       DEL PEAK 12(8P23.3) MUTATED DEL PEAK 12(8P23.3) WILD-TYPE
  FEMALE                          23                            85
  MALE                            42                           131
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(8P23.3) MUTATED       1                         0    64
  DEL PEAK 12(8P23.3) WILD-TYPE     4                         1   211
D35V13, multiclass
                           clus
vv                          DEL PEAK 12(8P23.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              64
                           clus
vv                          DEL PEAK 12(8P23.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               211
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                               cls
clus                              0   1
  DEL PEAK 12(8P23.3) MUTATED     0  65
  DEL PEAK 12(8P23.3) WILD-TYPE   3 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.3) MUTATED      0   65
  DEL PEAK 12(8P23.3) WILD-TYPE    3  209
                        clus
vv                       DEL PEAK 12(8P23.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          65
                        clus
vv                       DEL PEAK 12(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           209
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 13(9P23) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 13(9P23) MUTATED   87 97
  DEL PEAK 13(9P23) WILD-TYPE 50 36
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                        184                          86 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                         97                          36 
$`DEL PEAK 13(9P23) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.47       111.09        32.42        70.16        28.08        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       85.32        68.22        30.87         6.31        92.42        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       45.11        15.25        46.98        61.38        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J 
        9.34       103.59        26.37         5.39        80.22        41.10 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        13.94        95.38        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       23.11         4.01         2.89         9.90        11.31        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        51.12        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44Q 
       44.52        25.15         4.93         6.64         7.00        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
        0.20         0.00        13.22        11.57        10.55         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
        1.12         1.35         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        9.21         1.18        37.97        11.15        38.63         8.55 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
        1.08         9.50        12.03         8.09         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 
        2.43         8.68         8.09        11.31         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD 
       13.02        36.33         8.84        98.27         6.18         9.53 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       111.78       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       26.99        29.65        27.16       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       30.15        13.81        15.95        12.72         3.22        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       16.14        22.22        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       12.95         5.72        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.11        34.88        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
        9.57        36.07        17.72         1.87         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       11.74         9.04        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        4.90         6.71         3.58        64.47         3.45        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       14.24         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       11.08        30.87        47.38         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       40.64        27.39         0.82        53.85         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
       28.73        10.78         5.98         6.41         0.99         0.13 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26A 
        0.16         7.23        12.85        31.33        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        10.65        11.05         5.79 

$`DEL PEAK 13(9P23) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
        8.52       110.79        22.55        45.83        81.24         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        88.50        69.90        11.41         7.50        36.16 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F 
       64.44       114.67        46.32        82.29        13.32        42.71 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D9-A6EC TCGA-DA-A1I0 
       15.09        17.72        20.48        52.01        13.22        10.03 
TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5KH 
       36.69        22.36        19.36        17.56        14.83         0.13 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A29A 
        0.00         0.20         6.31        12.20         5.13         7.99 
TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.90         4.41        27.12         8.84        49.22        23.90 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME 
       19.43        16.01        34.98         2.70        47.51        29.46 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
       44.25        63.42        21.60        23.05         5.56        25.84 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19A 
       22.92        21.60        27.35         0.46        38.40        76.41 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ET 
      114.15         4.21        78.44        11.80        13.08         6.58 
TCGA-FR-A7U9 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        5.36        23.80        15.52        19.53         7.17        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FD 
       12.89        52.08         8.68         5.23        14.20         2.27 
TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        0.20         0.43         9.90        24.85        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A4U8 
       16.24        11.84 

  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                          0                           0 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                     124.31                      114.67 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                     13.085                      17.640 
[1] "0.0 - 124.3 (13.1)" "0.0 - 114.7 (17.6)"
[1] "hr=" "1.4"
D36V2, survival
                             sevent
clus2                          0  1
  DEL PEAK 13(9P23) MUTATED   89 98
  DEL PEAK 13(9P23) WILD-TYPE 53 36
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                        187                          89 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                         98                          36 
$`DEL PEAK 13(9P23) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.57       112.04       112.57        71.80        28.08        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
      103.10       168.00        48.76        12.10       171.58        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       45.11        58.06        46.98        86.93        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J 
        9.34       103.59        39.75        21.47       161.85       131.90 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        15.06       110.93       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      125.19        54.67         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       25.18        22.95        48.89        36.03       117.21       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
      176.55        35.93       107.34        53.92        65.92        68.09 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       10.49        13.87        10.16        45.11         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
       29.82        27.22        94.98        33.73        14.70         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C 
      109.64       151.27        78.87       168.26        13.55        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       13.97        39.62        72.07         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        55.92       345.96        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       46.82        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      135.95       208.04        48.72        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        13.91        14.30        55.59        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      129.27        19.76        47.28        16.96       204.66       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      203.05       167.90        47.54       248.65       103.56       136.47 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH 
      138.81       172.18        64.08        34.32        53.19       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      148.08        31.40        35.44        13.94         9.17        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L 
       48.89        12.59        13.02        26.37       152.35       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       23.34        20.15        31.27        32.05       247.04        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       33.21        92.98       174.21         4.90       210.08        15.16 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92        48.59       228.59        20.91         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
       48.85       357.37        53.52        15.45        32.75       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55        11.41       148.80        53.16        49.48        27.09 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67        28.73        12.43        26.73 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
       49.45        22.92        47.54         0.16         7.23        14.04 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X 
      117.93        62.79        32.48        39.58        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

$`DEL PEAK 13(9P23) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       16.67       133.25        31.59        90.90        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53        69.90        11.87       113.52        42.08 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F 
       66.08       130.72        46.32       166.52        60.23        43.69 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D9-A148 TCGA-D9-A1JW 
       40.14        18.38        51.68       135.75       151.53         3.65 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 
       66.25        20.38        61.18        23.44        28.60       215.44 
TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z 
       15.68        17.85        35.01         6.35        12.20         8.65 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M 
       26.89        68.15        63.35        80.61        32.19        44.35 
TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT 
       14.47       102.90        24.43        89.33        54.74        44.88 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MQ 
       28.83        61.51       103.27       103.20        96.23        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD 
       41.59        53.26        25.84       127.20        36.95        27.35 
TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A1A1 
       33.40        50.76        77.75       268.93         6.44        79.99 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       43.82        16.37        80.32         7.00       202.65        28.08 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU 
       40.27         9.70        47.38        23.93        74.73        26.56 
TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A3OT 
       27.02       174.84        77.88         0.20         2.40         9.90 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 
      120.46        84.72        10.13        64.44        46.36 

  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                       0.16                        0.20 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                     357.37                      268.93 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                      48.76                       44.88 
[1] "0.2 - 357.4 (48.8)" "0.2 - 268.9 (44.9)"
[1] "hr=" "1.1"
D36V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 13(9P23) MUTATED                   27             2
  DEL PEAK 13(9P23) WILD-TYPE                 10             2
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 13(9P23) MUTATED                                          43
  DEL PEAK 13(9P23) WILD-TYPE                                        17
                             vv
clus                          REGIONAL LYMPH NODE
  DEL PEAK 13(9P23) MUTATED                   118
  DEL PEAK 13(9P23) WILD-TYPE                  61
D36V4, multiclass
                                           clus
vv                                          DEL PEAK 13(9P23) MUTATED
  DISTANT METASTASIS                                               27
  PRIMARY TUMOR                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        43
  REGIONAL LYMPH NODE                                             118
                                           clus
vv                                          DEL PEAK 13(9P23) WILD-TYPE
  DISTANT METASTASIS                                                 10
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          17
  REGIONAL LYMPH NODE                                                61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 13(9P23) MUTATED             9       4      15        6       16
  DEL PEAK 13(9P23) WILD-TYPE           1       2       8        4        9
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 13(9P23) MUTATED         13         8        10         7        22
  DEL PEAK 13(9P23) WILD-TYPE        4         2         4         3        10
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 13(9P23) MUTATED            7         16         31        8
  DEL PEAK 13(9P23) WILD-TYPE          7          7         17        4
D36V5, multiclass
             clus
vv            DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  I OR II NOS                         9                           1
  STAGE 0                             4                           2
  STAGE I                            15                           8
  STAGE IA                            6                           4
  STAGE IB                           16                           9
  STAGE II                           13                           4
  STAGE IIA                           8                           2
  STAGE IIB                          10                           4
  STAGE IIC                           7                           3
  STAGE III                          22                          10
  STAGE IIIA                          7                           7
  STAGE IIIB                         16                           7
  STAGE IIIC                         31                          17
  STAGE IV                            8                           4
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 13(9P23) MUTATED      34 44 37 37
  DEL PEAK 13(9P23) WILD-TYPE    19 16 18 20
D36V6, multiclass
       clus
vv      DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  T0+T1                        34                          19
  T2                           44                          16
  T3                           37                          18
  T4                           37                          20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 13(9P23) MUTATED   99 35 19 23
  DEL PEAK 13(9P23) WILD-TYPE 42 16 13 14
D36V7, multiclass
    clus
vv   DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  N0                        99                          42
  N1                        35                          16
  N2                        19                          13
  N3                        23                          14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  DEL PEAK 13(9P23) MUTATED   172   1   1   1   5
  DEL PEAK 13(9P23) WILD-TYPE  80   3   1   1   0
D36V8, multiclass
     clus
vv    DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  M0                        172                          80
  M1                          1                           3
  M1A                         1                           1
  M1B                         1                           1
  M1C                         5                           0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                             cls
clus                           0  1
  DEL PEAK 13(9P23) MUTATED   70 49
  DEL PEAK 13(9P23) WILD-TYPE 34 23
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(9P23) MUTATED     70   49
  DEL PEAK 13(9P23) WILD-TYPE   34   23
     clus
vv    DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  NO                         70                          34
  YES                        49                          23
[1] 2 2
[1] FALSE
D36V10, binary
                             cls
clus                            0   1
  DEL PEAK 13(9P23) MUTATED    22 169
  DEL PEAK 13(9P23) WILD-TYPE  12  78
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(9P23) MUTATED     22  169
  DEL PEAK 13(9P23) WILD-TYPE   12   78
     clus
vv    DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  NO                         22                          12
  YES                       169                          78
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, binary
                             cls
clus                            0   1
  DEL PEAK 13(9P23) MUTATED    79 112
  DEL PEAK 13(9P23) WILD-TYPE  29  61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(9P23) MUTATED     79  112
  DEL PEAK 13(9P23) WILD-TYPE   29   61
        clus
vv       DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  FEMALE                        79                          29
  MALE                         112                          61
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(9P23) MUTATED       3                         1   187
  DEL PEAK 13(9P23) WILD-TYPE     2                         0    88
D36V13, multiclass
                           clus
vv                          DEL PEAK 13(9P23) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                           187
                           clus
vv                          DEL PEAK 13(9P23) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                             cls
clus                            0   1
  DEL PEAK 13(9P23) MUTATED     0 188
  DEL PEAK 13(9P23) WILD-TYPE   3  86
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(9P23) MUTATED      0  188
  DEL PEAK 13(9P23) WILD-TYPE    3   86
                        clus
vv                       DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                       188                          86
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 14(9P21.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(9P21.3) MUTATED    99 107
  DEL PEAK 14(9P21.3) WILD-TYPE  38  26
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          206                            64 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          107                            26 
$`DEL PEAK 14(9P21.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.47       111.09        32.42        70.16        28.08        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JL 
       85.32        68.22        69.90        30.87         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE 
       56.19        45.11        15.25        46.98        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       80.22        41.10         8.84        20.48        13.94        95.38 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        9.90        14.60        48.79        35.80        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        6.64         7.00        17.56        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
        0.00        13.22        11.57        10.55         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        1.35         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99        37.97        11.15        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41         1.08         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       47.21        30.08        35.54        28.31        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        5.42         1.15        13.02        36.33         8.84        98.27 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
        6.18         9.53         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
       56.02        25.08        26.99        29.65        27.16       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        5.72        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
       34.68         9.57        36.07        17.72        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
        1.51        12.62        11.74         9.04        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74         4.90         6.71         3.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       64.47         3.45        11.01        23.80        14.24         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        30.87        12.92        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 
       49.15        40.64        27.39         0.82        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
        0.20         0.99         0.13         0.16         7.23        12.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       31.33        84.72        15.42        12.16        14.70        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

$`DEL PEAK 14(9P21.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
        8.52       110.79        22.55        45.83        81.24         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO 
       21.14        88.50        11.41         7.50        36.16        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
      114.67        46.32        82.29        42.71        15.09        17.72 
TCGA-D3-A5GN TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A3F2 
       52.01        11.31        13.22        10.03        22.36        19.36 
TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 
       14.83         0.00         0.20         6.31        12.20         5.13 
TCGA-EE-A29B TCGA-EE-A29M TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK 
        9.90        27.12        49.22        23.90        19.43        16.01 
TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ 
       34.98         2.70        47.51        29.46        44.25        63.42 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A198 
       21.60        23.05         5.56        21.60        27.35        38.40 
TCGA-ER-A19A TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-FS-A1ZK 
       76.41        78.44        13.08         6.58        15.52        12.89 
TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A5DY TCGA-GF-A3OT 
       52.08         8.68         5.23         2.27         0.43         9.90 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 
       24.85        10.13        16.24        11.84 

  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                            0                             0 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                       124.31                        114.67 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                       13.185                        19.395 
[1] "0.0 - 124.3 (13.2)" "0.0 - 114.7 (19.4)"
[1] "hr=" "1.5"
D37V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(9P21.3) MUTATED   102 108
  DEL PEAK 14(9P21.3) WILD-TYPE  40  26
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          210                            66 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          108                            26 
$`DEL PEAK 14(9P21.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.57       112.04       112.57        71.80        28.08        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JL 
      103.10       168.00        69.90        48.76        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE 
       56.19        45.11        58.06        46.98        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      161.85       131.90        10.03        51.68        15.06       110.93 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV 
        6.41        11.34         3.25         9.90        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 
       61.18        53.92        65.92        68.09        10.49       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        17.85        45.11         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
       29.82        27.22        94.98        33.73        14.70         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        39.62        72.07        32.19         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        37.35        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 
       25.87       171.55        17.92        46.82        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD 
       55.59        94.82        21.67       129.27        19.76        47.28 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       144.76       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      248.65       103.56       136.47       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        64.08        34.32        53.19        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      148.08        31.40        35.44        13.94         9.17        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       37.25       148.18        43.82        23.34        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
        4.90       210.08        15.16         7.00       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        20.91         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38       101.26       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
      174.84        12.43        26.73        49.45         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 
       47.54         0.16         7.23        14.04       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        32.48        39.58        12.62       294.77         6.67 

$`DEL PEAK 14(9P21.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       16.67       133.25        31.59        90.90        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO 
       23.77       115.53        11.87       113.52        42.08        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
      130.72        46.32       166.52        43.69        40.14        18.38 
TCGA-D3-A5GN TCGA-D9-A1JW TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IB 
      135.75         3.65        25.18        66.25        20.38        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z 
       28.60        15.68        35.01         6.35        12.20         8.65 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29M TCGA-EE-A2A1 TCGA-EE-A2A2 
       26.89        68.15        80.61        44.35       102.90        24.43 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME 
       89.33        54.74        44.88        28.83        61.51       103.27 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3J5 
      103.20        96.23        43.23        41.59        53.26        36.95 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A3ET 
       27.35        50.76        77.75        79.99        16.37        80.32 
TCGA-FS-A1Z4 TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4FD 
       28.08        23.93        74.73        26.56        27.02        77.88 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 
        2.40         9.90       120.46        10.13        64.44        46.36 

  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                         0.16                          2.40 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                       357.37                        166.52 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                       48.805                        44.020 
[1] "0.2 - 357.4 (48.8)" "2.4 - 166.5 (44.0)"
[1] "hr=" "1"  
D37V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 14(9P21.3) MUTATED                   32             1
  DEL PEAK 14(9P21.3) WILD-TYPE                  5             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 14(9P21.3) MUTATED                                          46
  DEL PEAK 14(9P21.3) WILD-TYPE                                        14
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 14(9P21.3) MUTATED                   134
  DEL PEAK 14(9P21.3) WILD-TYPE                  45
D37V4, multiclass
                                           clus
vv                                          DEL PEAK 14(9P21.3) MUTATED
  DISTANT METASTASIS                                                 32
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          46
  REGIONAL LYMPH NODE                                               134
                                           clus
vv                                          DEL PEAK 14(9P21.3) WILD-TYPE
  DISTANT METASTASIS                                                    5
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            14
  REGIONAL LYMPH NODE                                                  45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 14(9P21.3) MUTATED             9       4      17        8       17
  DEL PEAK 14(9P21.3) WILD-TYPE           1       2       6        2        8
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 14(9P21.3) MUTATED         14         9        10         8
  DEL PEAK 14(9P21.3) WILD-TYPE        3         1         4         2
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 14(9P21.3) MUTATED          26          8         18         34
  DEL PEAK 14(9P21.3) WILD-TYPE         6          6          5         14
                               vv
clus                            STAGE IV
  DEL PEAK 14(9P21.3) MUTATED         10
  DEL PEAK 14(9P21.3) WILD-TYPE        2
D37V5, multiclass
             clus
vv            DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  I OR II NOS                           9                             1
  STAGE 0                               4                             2
  STAGE I                              17                             6
  STAGE IA                              8                             2
  STAGE IB                             17                             8
  STAGE II                             14                             3
  STAGE IIA                             9                             1
  STAGE IIB                            10                             4
  STAGE IIC                             8                             2
  STAGE III                            26                             6
  STAGE IIIA                            8                             6
  STAGE IIIB                           18                             5
  STAGE IIIC                           34                            14
  STAGE IV                             10                             2
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 14(9P21.3) MUTATED      43 46 43 39
  DEL PEAK 14(9P21.3) WILD-TYPE    10 14 12 18
D37V6, multiclass
       clus
vv      DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  T0+T1                          43                            10
  T2                             46                            14
  T3                             43                            12
  T4                             39                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 14(9P21.3) MUTATED   109  40  23  26
  DEL PEAK 14(9P21.3) WILD-TYPE  32  11   9  11
D37V7, multiclass
    clus
vv   DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  N0                         109                            32
  N1                          40                            11
  N2                          23                             9
  N3                          26                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  DEL PEAK 14(9P21.3) MUTATED   191   3   1   2   5
  DEL PEAK 14(9P21.3) WILD-TYPE  61   1   1   0   0
D37V8, multiclass
     clus
vv    DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  M0                          191                            61
  M1                            3                             1
  M1A                           1                             1
  M1B                           2                             0
  M1C                           5                             0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                               cls
clus                             0  1
  DEL PEAK 14(9P21.3) MUTATED   77 55
  DEL PEAK 14(9P21.3) WILD-TYPE 27 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED     77   55
  DEL PEAK 14(9P21.3) WILD-TYPE   27   17
     clus
vv    DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  NO                           77                            27
  YES                          55                            17
[1] 2 2
[1] FALSE
D37V10, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED    29 185
  DEL PEAK 14(9P21.3) WILD-TYPE   5  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED     29  185
  DEL PEAK 14(9P21.3) WILD-TYPE    5   62
     clus
vv    DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  NO                           29                             5
  YES                         185                            62
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED    89 125
  DEL PEAK 14(9P21.3) WILD-TYPE  19  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED     89  125
  DEL PEAK 14(9P21.3) WILD-TYPE   19   48
        clus
vv       DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  FEMALE                          89                            19
  MALE                           125                            48
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9P21.3) MUTATED       4                         1   209
  DEL PEAK 14(9P21.3) WILD-TYPE     1                         0    66
D37V13, multiclass
                           clus
vv                          DEL PEAK 14(9P21.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             209
                           clus
vv                          DEL PEAK 14(9P21.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED     0 210
  DEL PEAK 14(9P21.3) WILD-TYPE   3  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED      0  210
  DEL PEAK 14(9P21.3) WILD-TYPE    3   64
                        clus
vv                       DEL PEAK 14(9P21.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                         210
                        clus
vv                       DEL PEAK 14(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            64
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 15(10P15.3) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(10P15.3) MUTATED   70 80
  DEL PEAK 15(10P15.3) WILD-TYPE 67 53
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                           150                            120 
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                            80                             53 
$`DEL PEAK 15(10P15.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       10.29        88.50        69.90        11.41         7.50         6.31 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF 
       56.19        64.44        45.11        46.98        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
        9.34        26.37         5.39        42.71        41.10        17.72 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z3 
       13.94        52.01        47.87         1.55        23.11         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        9.90        11.31        14.60        35.80        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       17.56         0.20         0.00         6.31         8.12         1.12 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29G 
        5.13         4.31        36.07         9.21         1.18         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         6.48         8.68         8.09        23.90         9.67 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       39.39        34.92        47.21        30.08        19.43        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M6 
       33.83        30.84         5.42         1.15        13.02        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
        2.70         6.18        44.25         7.96        14.56       111.78 
TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       56.02        27.16         5.56       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       30.15        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
       16.14        22.22         0.46        13.94        33.60         5.72 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
        3.52        11.90       114.15        34.88        13.45        34.68 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       36.07        17.72        11.80         1.87         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90         6.71         3.58         3.45        23.80        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.33         7.30        20.38         8.22        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
       30.87        12.92        47.38         8.65         8.81         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 
       27.39         0.82         7.36        28.73         7.23        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       10.13        16.24        15.42        12.16        10.65        11.05 

$`DEL PEAK 15(10P15.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
        8.52        22.55        45.83        81.24        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3BZ 
       21.14        68.22        30.87        36.16        92.42       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MR 
       15.25        46.32        82.29        61.38         6.31       103.59 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GS 
       80.22        15.09         8.84        20.48        95.38         6.97 
TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC 
        4.01        13.22        48.79        10.03        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       19.36         7.00        14.83        13.15         0.13         0.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       13.22         0.20        11.57        10.55         1.35        12.20 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        4.34         5.13         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       38.63         8.84         2.43        11.31        49.22         8.94 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU 
       34.29        17.98        16.01        35.54        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2ML 
        8.84        47.51         9.53        29.46        63.42       111.91 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC 
       25.08        26.99        21.60        29.65        23.05        25.84 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       13.81        15.95        27.35        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19J 
       38.40        76.41        25.18         3.78        11.11         4.21 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-FR-A44A 
       28.60        42.84         9.57        78.44        13.08        85.74 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE 
        5.36        64.47        11.01        15.52         3.39        19.53 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 
       12.89        52.08        49.15        40.64         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        3.22        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       12.85        24.85        84.72        14.70        11.84         5.79 

  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                        124.31                         114.67 
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                        13.385                         15.170 
[1] "0.0 - 124.3 (13.4)" "0.0 - 114.7 (15.2)"
[1] "hr=" "1.3"
D38V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(10P15.3) MUTATED   70 80
  DEL PEAK 15(10P15.3) WILD-TYPE 72 54
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                           150                            126 
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                            80                             54 
$`DEL PEAK 15(10P15.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       43.43       115.53        69.90        11.87       113.52        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF 
       56.19        66.08        45.11        46.98        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
        9.34        39.75        21.47        43.69       131.90        18.38 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z3 
       15.06       135.75       137.92       166.19       125.19         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        9.90        25.18        22.95        36.03       117.21       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
      215.44        10.16        35.01         8.65        94.98        33.73 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29G 
       68.15         4.96       109.64       168.26        13.55        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
       55.92       345.96       171.55        17.92        24.43        39.29 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       47.54       135.95       208.04        48.72        89.33        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M6 
       90.97       101.95        13.91        14.30        55.59       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       28.83        19.76       103.20        16.96       204.66       144.76 
TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      167.90       136.47        53.26       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       54.51       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
       34.32        53.19        33.40       101.79       148.08         9.17 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
       12.59        13.02       268.93       152.35       131.51       162.08 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       37.25       148.18        43.82        23.34        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       210.08        15.16        48.59       202.65        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.79        27.72       357.37        53.52        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
       32.75        47.38       101.26       133.55        11.41        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 
       49.48        27.09        66.67        28.73         7.23       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       10.13        64.44        62.79        32.48        12.62       294.77 

$`DEL PEAK 15(10P15.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       16.67        31.59        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3BZ 
       23.77       168.00        48.76        42.08       171.58       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MR 
       58.06        46.32       166.52        86.93        13.87       103.59 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GS 
      161.85        40.14        10.03        51.68       110.93         7.43 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6EC 
      151.53        54.67         3.65         6.41        11.34        66.25 
TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       48.89        20.38        23.44        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       15.68        13.87        17.85        45.11         3.55        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
        6.35        12.20        29.82        27.22        14.70        26.89 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      151.27        78.87        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       39.62        14.47        25.87        46.82       102.90        58.75 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU 
       67.43       314.56        54.74        79.66        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2ML 
       21.67        61.51        47.28       103.27        96.23       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC 
       47.54       248.65        43.23       103.56        41.59        25.84 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       13.81        23.47        27.35        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19J 
       50.76        77.75        98.40        48.89        26.37         6.44 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-FR-A44A 
       61.05        44.05        50.89        79.99        16.37       174.21 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE 
        7.00       216.92       228.59        28.08        48.85        40.27 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 
       23.93        74.73       148.80        53.16        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       50.14       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16         2.40         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       14.04       120.46        84.72        39.58        46.36         6.67 

  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                          2.60                           0.16 
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                        357.37                         314.56 
  DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE 
                        51.335                         47.050 
[1] "2.6 - 357.4 (51.3)" "0.2 - 314.6 (47.0)"
[1] "hr=" "1"  
D38V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 15(10P15.3) MUTATED                   22             2
  DEL PEAK 15(10P15.3) WILD-TYPE                 15             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 15(10P15.3) MUTATED                                          41
  DEL PEAK 15(10P15.3) WILD-TYPE                                        19
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 15(10P15.3) MUTATED                    89
  DEL PEAK 15(10P15.3) WILD-TYPE                  90
D38V4, multiclass
                                           clus
vv                                          DEL PEAK 15(10P15.3) MUTATED
  DISTANT METASTASIS                                                  22
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           41
  REGIONAL LYMPH NODE                                                 89
                                           clus
vv                                          DEL PEAK 15(10P15.3) WILD-TYPE
  DISTANT METASTASIS                                                    15
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             19
  REGIONAL LYMPH NODE                                                   90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 15(10P15.3) MUTATED             7       3      12        6       15
  DEL PEAK 15(10P15.3) WILD-TYPE           3       3      11        4       10
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 15(10P15.3) MUTATED         10         4         6         4
  DEL PEAK 15(10P15.3) WILD-TYPE        7         6         8         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 15(10P15.3) MUTATED          19         10         12         28
  DEL PEAK 15(10P15.3) WILD-TYPE        13          4         11         20
                                vv
clus                             STAGE IV
  DEL PEAK 15(10P15.3) MUTATED          6
  DEL PEAK 15(10P15.3) WILD-TYPE        6
D38V5, multiclass
             clus
vv            DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE
  I OR II NOS                            7                              3
  STAGE 0                                3                              3
  STAGE I                               12                             11
  STAGE IA                               6                              4
  STAGE IB                              15                             10
  STAGE II                              10                              7
  STAGE IIA                              4                              6
  STAGE IIB                              6                              8
  STAGE IIC                              4                              6
  STAGE III                             19                             13
  STAGE IIIA                            10                              4
  STAGE IIIB                            12                             11
  STAGE IIIC                            28                             20
  STAGE IV                               6                              6
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 15(10P15.3) MUTATED      29 36 23 37
  DEL PEAK 15(10P15.3) WILD-TYPE    24 24 32 20
D38V6, multiclass
       clus
vv      DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE
  T0+T1                           29                             24
  T2                              36                             24
  T3                              23                             32
  T4                              37                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 15(10P15.3) MUTATED   79 31 16 19
  DEL PEAK 15(10P15.3) WILD-TYPE 62 20 16 18
D38V7, multiclass
    clus
vv   DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE
  N0                           79                             62
  N1                           31                             20
  N2                           16                             16
  N3                           19                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 15(10P15.3) MUTATED   140   1   1   1   3
  DEL PEAK 15(10P15.3) WILD-TYPE 112   3   1   1   2
D38V8, multiclass
     clus
vv    DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE
  M0                           140                            112
  M1                             1                              3
  M1A                            1                              1
  M1B                            1                              1
  M1C                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                                cls
clus                              0  1
  DEL PEAK 15(10P15.3) MUTATED   55 42
  DEL PEAK 15(10P15.3) WILD-TYPE 49 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(10P15.3) MUTATED     55   42
  DEL PEAK 15(10P15.3) WILD-TYPE   49   30
     clus
vv    DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE
  NO                            55                             49
  YES                           42                             30
[1] 2 2
[1] FALSE
D38V10, binary
                                cls
clus                               0   1
  DEL PEAK 15(10P15.3) MUTATED    18 136
  DEL PEAK 15(10P15.3) WILD-TYPE  16 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(10P15.3) MUTATED     18  136
  DEL PEAK 15(10P15.3) WILD-TYPE   16  111
     clus
vv    DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE
  NO                            18                             16
  YES                          136                            111
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, binary
                                cls
clus                              0  1
  DEL PEAK 15(10P15.3) MUTATED   64 90
  DEL PEAK 15(10P15.3) WILD-TYPE 44 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(10P15.3) MUTATED     64   90
  DEL PEAK 15(10P15.3) WILD-TYPE   44   83
        clus
vv       DEL PEAK 15(10P15.3) MUTATED DEL PEAK 15(10P15.3) WILD-TYPE
  FEMALE                           64                             44
  MALE                             90                             83
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(10P15.3) MUTATED       1                         0   153
  DEL PEAK 15(10P15.3) WILD-TYPE     4                         1   122
D38V13, multiclass
                           clus
vv                          DEL PEAK 15(10P15.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              153
                           clus
vv                          DEL PEAK 15(10P15.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                                cls
clus                               0   1
  DEL PEAK 15(10P15.3) MUTATED     1 152
  DEL PEAK 15(10P15.3) WILD-TYPE   2 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(10P15.3) MUTATED      1  152
  DEL PEAK 15(10P15.3) WILD-TYPE    2  122
                        clus
vv                       DEL PEAK 15(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          152
                        clus
vv                       DEL PEAK 15(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            122
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 16(10Q23.31) MUTATION ANALYSIS
D39V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(10Q23.31) MUTATED   85 83
  DEL PEAK 16(10Q23.31) WILD-TYPE 52 50
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                            168                             102 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             83                              50 
$`DEL PEAK 16(10Q23.31) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       22.55        88.50        69.90        11.41         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       92.42        56.19        64.44        45.11        15.25        46.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       61.38        13.32        24.00         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
        5.39        42.71        41.10        17.72         8.84        13.94 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       52.01        47.87         1.55         6.97        23.11         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 
        9.90        11.31        13.22        14.60        35.80        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y 
       17.56        14.83         0.20         0.00        13.22        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         8.12         1.12         4.31        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        9.21         1.18        11.15         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       27.12        12.03         8.09         6.48         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       17.98        34.92        47.21        30.08        19.43        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       33.83        30.84         5.42         1.15        13.02        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH 
       98.27         2.70         6.18         9.53        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA 
       14.56       111.78        56.02        26.99         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
        3.22        22.92        21.60        16.14        22.22         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       13.94        33.60        31.40         5.72         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2NC 
       11.90        34.88        13.45        34.68        36.07        11.80 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
        1.51        12.62        11.74        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         4.90         6.71         3.58        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       14.24         7.33         7.30        20.38         8.22        11.08 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
       30.87        12.92        47.38         8.65         8.81         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3I3 
       27.39         0.82         7.36        28.73         5.98         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.13         0.16         7.23        12.85        24.85        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       10.13        16.24        12.16        11.84        10.65        11.05 

$`DEL PEAK 16(10Q23.31) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
        8.52        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3BZ TCGA-D3-A3C8 
       21.14        68.22        30.87        36.16       114.67        46.32 
TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL 
       82.29         6.31        80.22        15.09        20.48        95.38 
TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC 
        4.01        48.79        51.12        10.03        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A6L9 
       19.36         7.00        13.15         0.13         0.00         0.20 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A 
       11.57         1.35        12.20         5.13         4.34         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
        9.90        37.97        38.63         9.50         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 
        2.43        49.22        16.01        35.54        34.98         8.84 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ 
       47.51        29.46        63.42       111.91        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J7 TCGA-EE-A3JD 
       29.65        27.16        23.05        25.84        21.60        27.35 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F 
       18.61        12.95        38.40        76.41        25.18        11.11 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
      114.15         4.21        28.60        42.84         9.57        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U9 
       78.44         1.87        13.08         9.04         6.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
       64.47         3.45        15.52         3.39        19.53         7.17 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 
       12.89        52.08        49.15        40.64         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
        3.22        14.20        10.78         6.41         2.27         0.99 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
        0.43         9.90        84.72        15.42        14.70         5.79 

  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              0                               0 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         124.31                          114.67 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         13.385                          15.765 
[1] "0.0 - 124.3 (13.4)" "0.0 - 114.7 (15.8)"
[1] "hr=" "1.1"
D39V2, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(10Q23.31) MUTATED   88 84
  DEL PEAK 16(10Q23.31) WILD-TYPE 54 50
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                            172                             104 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                             84                              50 
$`DEL PEAK 16(10Q23.31) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       31.59       115.53        69.90        11.87       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        56.19        66.08        45.11        58.06        46.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
       21.47        43.69       131.90        18.38        10.03        15.06 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       54.67         6.41         3.25         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       22.95        36.03       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R 
       61.18        53.92        65.92       215.44        15.68        10.16 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       35.01         3.55        52.01        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       33.73         4.96       109.64        78.87       168.26        13.55 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       13.97        72.07        32.19         2.60        44.35        56.42 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
       37.35       345.96       171.55        17.92        46.82        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      208.04        48.72        89.33        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        14.30        55.59        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       19.76        47.28       103.20        16.96       204.66       144.76 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      167.90       248.65        53.26       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        34.32        53.19        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
       31.40         9.17        48.89        12.59        13.02       152.35 
TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
      131.51       162.08        37.25        43.82        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       32.05        46.98        33.21        92.98       174.21         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
      210.08        15.16       228.59       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       27.72       357.37        53.52        15.45        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26       133.55        11.41        26.56        49.48        27.09 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67        28.73        26.73         0.20        47.54         0.16 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        7.23        14.04       120.46       117.93        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       32.48        46.36        12.62       294.77 

$`DEL PEAK 16(10Q23.31) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       16.67        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3BZ TCGA-D3-A3C8 
       23.77       168.00        48.76        42.08       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL 
      166.52        13.87       161.85        40.14        51.68       110.93 
TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB 
        3.65        11.34        48.89       117.21        20.38        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       68.09        28.60        10.49        13.87        17.85        45.11 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.35        12.20        29.82        14.70        26.89        68.15 
TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N 
      151.27        63.35        80.61        47.84        39.62        18.61 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL 
       14.47        55.92        25.87       102.90        54.74        79.66 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2ML 
       44.88        21.67        61.51       103.27        96.23       203.05 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
       47.54        43.23       103.56       136.47        41.59        25.84 
TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       64.08        27.35        35.44        13.94        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       98.40        26.37       268.93         6.44        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES 
       50.89       148.18        79.99        23.34        16.37       247.04 
TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZB 
       80.32         7.00       216.92        48.59        28.08        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT 
       40.27         9.70        23.93        74.73       148.80        53.16 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC 
       27.02        77.82        50.14       174.84        12.43        49.45 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A268 
       77.88        22.92         2.40         9.90        84.72        62.79 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                           0.16                            2.40 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         357.37                          268.93 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         47.540                          48.215 
[1] "0.2 - 357.4 (47.5)" "2.4 - 268.9 (48.2)"
[1] "hr=" "1.1"
D39V3, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 16(10Q23.31) MUTATED                   23             3
  DEL PEAK 16(10Q23.31) WILD-TYPE                 14             1
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 16(10Q23.31) MUTATED                                          44
  DEL PEAK 16(10Q23.31) WILD-TYPE                                        16
                                 vv
clus                              REGIONAL LYMPH NODE
  DEL PEAK 16(10Q23.31) MUTATED                   105
  DEL PEAK 16(10Q23.31) WILD-TYPE                  74
D39V4, multiclass
                                           clus
vv                                          DEL PEAK 16(10Q23.31) MUTATED
  DISTANT METASTASIS                                                   23
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            44
  REGIONAL LYMPH NODE                                                 105
                                           clus
vv                                          DEL PEAK 16(10Q23.31) WILD-TYPE
  DISTANT METASTASIS                                                     14
  PRIMARY TUMOR                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                              16
  REGIONAL LYMPH NODE                                                    74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 16(10Q23.31) MUTATED             6       3      13        8       15
  DEL PEAK 16(10Q23.31) WILD-TYPE           4       3      10        2       10
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 16(10Q23.31) MUTATED         11         5         8         6
  DEL PEAK 16(10Q23.31) WILD-TYPE        6         5         6         4
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 16(10Q23.31) MUTATED          24         10         15         27
  DEL PEAK 16(10Q23.31) WILD-TYPE         8          4          8         21
                                 vv
clus                              STAGE IV
  DEL PEAK 16(10Q23.31) MUTATED          9
  DEL PEAK 16(10Q23.31) WILD-TYPE        3
D39V5, multiclass
             clus
vv            DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  I OR II NOS                             6                               4
  STAGE 0                                 3                               3
  STAGE I                                13                              10
  STAGE IA                                8                               2
  STAGE IB                               15                              10
  STAGE II                               11                               6
  STAGE IIA                               5                               5
  STAGE IIB                               8                               6
  STAGE IIC                               6                               4
  STAGE III                              24                               8
  STAGE IIIA                             10                               4
  STAGE IIIB                             15                               8
  STAGE IIIC                             27                              21
  STAGE IV                                9                               3
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 16(10Q23.31) MUTATED      37 37 29 40
  DEL PEAK 16(10Q23.31) WILD-TYPE    16 23 26 17
D39V6, multiclass
       clus
vv      DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  T0+T1                            37                              16
  T2                               37                              23
  T3                               29                              26
  T4                               40                              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 16(10Q23.31) MUTATED   84 38 19 20
  DEL PEAK 16(10Q23.31) WILD-TYPE 57 13 13 17
D39V7, multiclass
    clus
vv   DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  N0                            84                              57
  N1                            38                              13
  N2                            19                              13
  N3                            20                              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B M1C
  DEL PEAK 16(10Q23.31) MUTATED   156   2   1   2   5
  DEL PEAK 16(10Q23.31) WILD-TYPE  96   2   1   0   0
D39V8, multiclass
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  M0                            156                              96
  M1                              2                               2
  M1A                             1                               1
  M1B                             2                               0
  M1C                             5                               0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   61 47
  DEL PEAK 16(10Q23.31) WILD-TYPE 43 25
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     61   47
  DEL PEAK 16(10Q23.31) WILD-TYPE   43   25
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  NO                             61                              43
  YES                            47                              25
[1] 2 2
[1] FALSE
D39V10, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED    23 152
  DEL PEAK 16(10Q23.31) WILD-TYPE  11  95
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     23  152
  DEL PEAK 16(10Q23.31) WILD-TYPE   11   95
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  NO                             23                              11
  YES                           152                              95
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED   76 99
  DEL PEAK 16(10Q23.31) WILD-TYPE 32 74
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED     76   99
  DEL PEAK 16(10Q23.31) WILD-TYPE   32   74
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  FEMALE                            76                              32
  MALE                              99                              74
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10Q23.31) MUTATED       2                         0   173
  DEL PEAK 16(10Q23.31) WILD-TYPE     3                         1   102
D39V13, multiclass
                           clus
vv                          DEL PEAK 16(10Q23.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               173
                           clus
vv                          DEL PEAK 16(10Q23.31) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                 102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q23.31) MUTATED     1 172
  DEL PEAK 16(10Q23.31) WILD-TYPE   2 102
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      1  172
  DEL PEAK 16(10Q23.31) WILD-TYPE    2  102
                        clus
vv                       DEL PEAK 16(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           172
                        clus
vv                       DEL PEAK 16(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             102
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 17(10Q26.3) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(10Q26.3) MUTATED   88 85
  DEL PEAK 17(10Q26.3) WILD-TYPE 49 48
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                           173                             97 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                            85                             48 
$`DEL PEAK 17(10Q26.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       22.55        88.50        69.90        11.41         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
       92.42        56.19        45.11        15.25        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       24.00         9.34       103.59        26.37         5.39        42.71 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       41.10        17.72         8.84        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        1.55         6.97        23.11         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       13.22        14.60        35.80        51.12        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 
        9.99        44.52        36.69        25.15         4.93        17.56 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 
       14.83         0.20         0.00        13.22         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        1.12         4.31        36.07         5.13         9.21         1.18 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       11.15         8.55         4.41        27.12        12.03         8.09 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
        6.48         8.68         8.09        11.31        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       30.08        19.43        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      111.78        56.02        26.99         5.56       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
       22.92        21.60        21.60        16.14        22.22         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B 
       13.94        33.60        31.40        18.61         5.72        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
        3.78         3.52        11.90        34.88        13.45        34.68 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       36.07        17.72        11.80         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       11.74         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.90         6.71         3.58         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH 
       14.24         7.33         7.30        20.38        11.08        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       12.92        47.38         8.65         8.81         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TU 
        0.82         7.36        28.73         5.98         2.27         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         0.43         7.23        12.85        24.85        31.33 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       10.13        12.16        11.84        10.65        11.05 

$`DEL PEAK 17(10Q26.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
        8.52        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ 
       21.14        68.22        30.87        36.16        64.44       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H 
       46.98        46.32        82.29         6.31        80.22        15.09 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1IB 
       20.48        95.38         4.01        48.79        10.03        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
        6.64        19.36         7.00        13.15         0.13         0.00 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        0.20        11.57        10.55         1.35        12.20         5.13 
TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29L 
        4.34         7.99         9.90        37.97        38.63         1.08 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GK 
        9.50         8.84         9.99         2.43        49.22        16.01 
TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
       35.54        34.98        47.51        63.42       111.91        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JD 
       21.60        29.65        27.16        23.05        25.84        27.35 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
       12.95        38.40        76.41        11.11       114.15         4.21 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A3ES 
       28.60        42.84         9.57        78.44         1.87         9.04 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
        5.36        64.47        15.52         3.39         8.22        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ 
        7.17        12.89        52.08        49.15        40.64         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
       53.85         3.22        14.20        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        0.99         9.90        84.72        16.24        15.42        14.70 
TCGA-QB-A6FS 
        5.79 

  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                        124.31                         114.67 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                         13.45                          15.52 
[1] "0.0 - 124.3 (13.4)" "0.0 - 114.7 (15.5)"
[1] "hr=" "1.1"
D40V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(10Q26.3) MUTATED   91 85
  DEL PEAK 17(10Q26.3) WILD-TYPE 51 49
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                           176                            100 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                            85                             49 
$`DEL PEAK 17(10Q26.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       31.59       115.53        69.90        11.87       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
      171.58        56.19        45.11        58.06        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       24.53         9.34       103.59        39.75        21.47        43.69 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
      131.90        18.38        10.03        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
      166.19         7.43       125.19       151.53        54.67         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        66.25        22.95        36.03       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL 
       65.92       215.44        15.68        10.16        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B 
       52.01         8.65        94.98        33.73         4.96       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       78.87       168.26        13.55        13.97        72.07        32.19 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       44.35        56.42        37.35       345.96       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
      314.56       135.95       208.04        48.72        89.33        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       90.97       101.95        13.91        14.30        55.59        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67       129.27        28.83        19.76        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
      103.20        16.96       204.66       144.76       167.90       248.65 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31       122.73         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        53.19        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       35.44         9.17        98.40        48.89        12.59        13.02 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC 
      152.35       131.51       162.08        37.25       148.18        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        16.37        31.27        32.05        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       33.21        92.98       174.21         4.90       210.08        15.16 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59       202.65        20.91         7.79        27.72 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      357.37        15.45        32.75        47.38       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
       11.41        26.56        49.48        27.09        66.67        28.73 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO 
       26.73        77.88        47.54         0.16         2.40         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 
       14.04       120.46       117.93        10.13        32.48        46.36 
TCGA-GN-A4U9 TCGA-OD-A75X 
       12.62       294.77 

$`DEL PEAK 17(10Q26.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       16.67        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ 
       23.77       168.00        48.76        42.08        66.08       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H 
       46.98        46.32       166.52        13.87       161.85        40.14 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-DA-A1HV 
       51.68       110.93         3.65         6.41        11.34        48.89 
TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q 
       20.38        23.44        68.09        28.60        10.49        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.85        45.11         6.35        12.20        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B 
       14.70        26.89        68.15       151.27        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       47.84        39.62         2.60        18.61        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2MC 
       25.87       102.90        54.74        79.66        44.88        61.51 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       96.23       203.05        47.54        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JD TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       41.59        25.84        27.35        13.94        50.76        77.75 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       26.37       268.93         6.44        61.05        44.05        50.89 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A3ES TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1Z4 
       79.99        23.34       247.04         7.00       216.92        28.08 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
       48.85        53.52        40.27         9.70        23.93        74.73 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
      148.80        53.16        27.02        77.82        50.14       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GF-A3OT TCGA-GN-A265 
       12.43        49.45         0.20        22.92         9.90        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        39.58         6.67 

  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                          0.16                           0.20 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                        357.37                         268.93 
  DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE 
                        48.805                         46.650 
[1] "0.2 - 357.4 (48.8)" "0.2 - 268.9 (46.6)"
[1] "hr=" "1.2"
D40V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 17(10Q26.3) MUTATED                   22             4
  DEL PEAK 17(10Q26.3) WILD-TYPE                 15             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 17(10Q26.3) MUTATED                                          47
  DEL PEAK 17(10Q26.3) WILD-TYPE                                        13
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 17(10Q26.3) MUTATED                   107
  DEL PEAK 17(10Q26.3) WILD-TYPE                  72
D40V4, multiclass
                                           clus
vv                                          DEL PEAK 17(10Q26.3) MUTATED
  DISTANT METASTASIS                                                  22
  PRIMARY TUMOR                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           47
  REGIONAL LYMPH NODE                                                107
                                           clus
vv                                          DEL PEAK 17(10Q26.3) WILD-TYPE
  DISTANT METASTASIS                                                    15
  PRIMARY TUMOR                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             13
  REGIONAL LYMPH NODE                                                   72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 17(10Q26.3) MUTATED             7       3      17        8       15
  DEL PEAK 17(10Q26.3) WILD-TYPE           3       3       6        2       10
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 17(10Q26.3) MUTATED         11         4         8         6
  DEL PEAK 17(10Q26.3) WILD-TYPE        6         6         6         4
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 17(10Q26.3) MUTATED          24         10         14         28
  DEL PEAK 17(10Q26.3) WILD-TYPE         8          4          9         20
                                vv
clus                             STAGE IV
  DEL PEAK 17(10Q26.3) MUTATED          8
  DEL PEAK 17(10Q26.3) WILD-TYPE        4
D40V5, multiclass
             clus
vv            DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  I OR II NOS                            7                              3
  STAGE 0                                3                              3
  STAGE I                               17                              6
  STAGE IA                               8                              2
  STAGE IB                              15                             10
  STAGE II                              11                              6
  STAGE IIA                              4                              6
  STAGE IIB                              8                              6
  STAGE IIC                              6                              4
  STAGE III                             24                              8
  STAGE IIIA                            10                              4
  STAGE IIIB                            14                              9
  STAGE IIIC                            28                             20
  STAGE IV                               8                              4
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 17(10Q26.3) MUTATED      36 42 30 38
  DEL PEAK 17(10Q26.3) WILD-TYPE    17 18 25 19
D40V6, multiclass
       clus
vv      DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  T0+T1                           36                             17
  T2                              42                             18
  T3                              30                             25
  T4                              38                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 17(10Q26.3) MUTATED   89 37 19 21
  DEL PEAK 17(10Q26.3) WILD-TYPE 52 14 13 16
D40V7, multiclass
    clus
vv   DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  N0                           89                             52
  N1                           37                             14
  N2                           19                             13
  N3                           21                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 17(10Q26.3) MUTATED   160   1   1   2   5
  DEL PEAK 17(10Q26.3) WILD-TYPE  92   3   1   0   0
D40V8, multiclass
     clus
vv    DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  M0                           160                             92
  M1                             1                              3
  M1A                            1                              1
  M1B                            2                              0
  M1C                            5                              0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                                cls
clus                              0  1
  DEL PEAK 17(10Q26.3) MUTATED   63 46
  DEL PEAK 17(10Q26.3) WILD-TYPE 41 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q26.3) MUTATED     63   46
  DEL PEAK 17(10Q26.3) WILD-TYPE   41   26
     clus
vv    DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  NO                            63                             41
  YES                           46                             26
[1] 2 2
[1] FALSE
D40V10, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q26.3) MUTATED    21 159
  DEL PEAK 17(10Q26.3) WILD-TYPE  13  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q26.3) MUTATED     21  159
  DEL PEAK 17(10Q26.3) WILD-TYPE   13   88
     clus
vv    DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  NO                            21                             13
  YES                          159                             88
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q26.3) MUTATED    77 103
  DEL PEAK 17(10Q26.3) WILD-TYPE  31  70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q26.3) MUTATED     77  103
  DEL PEAK 17(10Q26.3) WILD-TYPE   31   70
        clus
vv       DEL PEAK 17(10Q26.3) MUTATED DEL PEAK 17(10Q26.3) WILD-TYPE
  FEMALE                           77                             31
  MALE                            103                             70
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(10Q26.3) MUTATED       1                         0   179
  DEL PEAK 17(10Q26.3) WILD-TYPE     4                         1    96
D40V13, multiclass
                           clus
vv                          DEL PEAK 17(10Q26.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              179
                           clus
vv                          DEL PEAK 17(10Q26.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q26.3) MUTATED     1 178
  DEL PEAK 17(10Q26.3) WILD-TYPE   2  96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q26.3) MUTATED      1  178
  DEL PEAK 17(10Q26.3) WILD-TYPE    2   96
                        clus
vv                       DEL PEAK 17(10Q26.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          178
                        clus
vv                       DEL PEAK 17(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             96
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 18(11P11.2) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(11P11.2) MUTATED   46 42
  DEL PEAK 18(11P11.2) WILD-TYPE 91 91
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                            88                            182 
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                            42                             91 
$`DEL PEAK 18(11P11.2) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       16.47        32.42        10.29        11.41        92.42        56.19 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A5GN 
       15.25        46.98        61.38         9.34         5.39        52.01 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
        1.55        23.11        11.31        48.79        35.80        39.19 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       44.52        25.15        17.56         0.20         0.13         0.00 
TCGA-EB-A5SH TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29C 
        0.00         1.35        36.07         4.34         1.18        37.97 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GE 
        2.43         8.09        23.90         9.67        34.29        34.92 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP 
       28.31         1.15        98.27        63.42        25.08        26.99 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 
       27.16         5.56       122.73        30.15        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       16.14        13.94        31.40        12.95         5.72         3.78 
TCGA-ER-A19D TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        3.52        36.07         1.87         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1ZA TCGA-FS-A1ZF TCGA-FS-A1ZH 
        1.71        18.41         4.90         7.30        11.08        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F5 TCGA-FS-A4F9 
       12.92        47.38         8.68        27.39        28.73        10.78 
TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        5.98         0.20         0.99        24.85        31.33        16.24 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X 
       12.16        14.70        10.65        11.05 

$`DEL PEAK 18(11P11.2) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
        8.52       111.09        70.16       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       45.83        81.24        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        69.90        30.87         7.50        36.16         6.31 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       64.44        45.11       114.67        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.00         6.31       103.59        26.37        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       95.38        47.87         6.97         4.01         2.89         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       13.22        14.60        51.12        10.03        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       14.83        13.15        13.22         0.20        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.12        12.20         5.13         4.31 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
        5.13         9.21         7.99         9.90        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
        8.55         4.41         9.99         6.48         8.68        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI 
       49.22         8.94        39.39        17.98        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        33.83        30.84         5.42 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33         8.84         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      111.78       111.91        56.02        21.60        29.65        23.05 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      124.31        25.84         3.68        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
        3.22        22.92        22.22        27.35         0.46        33.60 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F 
       18.61        38.40        76.41        25.18        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       34.68         9.57        17.72        78.44        11.80         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       13.08        12.62        11.74        85.74         6.71         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.36        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.17        12.89        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       40.64         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       14.20         6.41         2.27         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        9.90         7.23        12.85        84.72        10.13        15.42 
TCGA-GN-A4U8 TCGA-QB-A6FS 
       11.84         5.79 

  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                          0.00                           0.13 
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                         14.32                          14.07 
[1] "0.0 - 122.7 (14.3)" "0.1 - 124.3 (14.1)"
[1] "hr=" "1.1"
D41V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(11P11.2) MUTATED   47 43
  DEL PEAK 18(11P11.2) WILD-TYPE 95 91
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                            90                            186 
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                            43                             91 
$`DEL PEAK 18(11P11.2) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       16.57       112.57        43.43        11.87       171.58        56.19 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A5GN 
       58.06        46.98        86.93         9.34        21.47       135.75 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A6EA TCGA-DA-A1HV 
      166.19       125.19        54.67         6.41        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R 
       36.03       194.83       107.34        53.92       215.44        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C 
       17.85        45.11        35.01        14.70       109.64       151.27 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       13.55        47.84         2.60        44.35        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
       37.35        14.47        25.87        17.92        24.43        39.29 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MJ 
       67.43       135.95        75.48        14.30       129.27        96.23 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE 
       47.54       248.65       136.47        53.26       122.73        54.51 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 
       36.95        64.08        34.32       101.79        31.40        13.94 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES 
        9.17        48.89        12.59        37.25        23.34       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1ZA 
       80.32        46.98        33.21        92.98         4.90        27.72 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-FS-A1ZW 
       15.45        32.75        47.38       101.26        26.56        49.48 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A262 
       28.73        12.43        26.73         0.20        22.92       120.46 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X 
      117.93        64.44        32.48        39.58        12.62       294.77 

$`DEL PEAK 18(11P11.2) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.04        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        69.90        48.76       113.52        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       66.08        45.11       130.72        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53        13.87       103.59        39.75       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A3Z1 
      110.93       137.92         7.43       151.53         3.65        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
        3.25         9.90        66.25        22.95       117.21        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93        61.18        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5UN 
       28.60        10.49        15.68        13.87         3.55        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        6.35        12.20        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H 
       33.73        26.89        68.15         4.96        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        13.97        39.62        72.07        32.19 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       55.92       345.96       171.55        46.82       102.90        58.75 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       47.54       314.56       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        90.97       101.95        13.91        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82        21.67        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      167.90        43.23       103.56        41.59       124.31        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       53.19        27.35        33.40       148.08        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        98.40        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        43.82        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       32.05       174.21       210.08        15.16         7.00       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK 
       48.85       357.37        53.52        40.27         9.70        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZY 
       74.73       133.55        11.41       148.80        53.16        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FC 
       27.02        77.82        50.14        66.67       174.84        49.45 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       77.88        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-QB-A6FS 
       14.04        84.72        10.13        62.79        46.36         6.67 

  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                          0.20                           0.16 
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                        294.77                         357.37 
  DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE 
                        44.730                         49.795 
[1] "0.2 - 294.8 (44.7)" "0.2 - 357.4 (49.8)"
[1] "hr=" "1.1"
D41V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 18(11P11.2) MUTATED                   13             1
  DEL PEAK 18(11P11.2) WILD-TYPE                 24             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 18(11P11.2) MUTATED                                          23
  DEL PEAK 18(11P11.2) WILD-TYPE                                        37
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 18(11P11.2) MUTATED                    53
  DEL PEAK 18(11P11.2) WILD-TYPE                 126
D41V4, multiclass
                                           clus
vv                                          DEL PEAK 18(11P11.2) MUTATED
  DISTANT METASTASIS                                                  13
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           23
  REGIONAL LYMPH NODE                                                 53
                                           clus
vv                                          DEL PEAK 18(11P11.2) WILD-TYPE
  DISTANT METASTASIS                                                    24
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             37
  REGIONAL LYMPH NODE                                                  126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 18(11P11.2) MUTATED             4       1       8        2       10
  DEL PEAK 18(11P11.2) WILD-TYPE           6       5      15        8       15
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 18(11P11.2) MUTATED          3         0         4         6
  DEL PEAK 18(11P11.2) WILD-TYPE       14        10        10         4
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 18(11P11.2) MUTATED          13          4          7         16
  DEL PEAK 18(11P11.2) WILD-TYPE        19         10         16         32
                                vv
clus                             STAGE IV
  DEL PEAK 18(11P11.2) MUTATED          5
  DEL PEAK 18(11P11.2) WILD-TYPE        7
D41V5, multiclass
             clus
vv            DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE
  I OR II NOS                            4                              6
  STAGE 0                                1                              5
  STAGE I                                8                             15
  STAGE IA                               2                              8
  STAGE IB                              10                             15
  STAGE II                               3                             14
  STAGE IIA                              0                             10
  STAGE IIB                              4                             10
  STAGE IIC                              6                              4
  STAGE III                             13                             19
  STAGE IIIA                             4                             10
  STAGE IIIB                             7                             16
  STAGE IIIC                            16                             32
  STAGE IV                               5                              7
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 18(11P11.2) MUTATED      17 21 12 24
  DEL PEAK 18(11P11.2) WILD-TYPE    36 39 43 33
D41V6, multiclass
       clus
vv      DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE
  T0+T1                           17                             36
  T2                              21                             39
  T3                              12                             43
  T4                              24                             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 18(11P11.2) MUTATED   44 19  9 11
  DEL PEAK 18(11P11.2) WILD-TYPE 97 32 23 26
D41V7, multiclass
    clus
vv   DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE
  N0                           44                             97
  N1                           19                             32
  N2                            9                             23
  N3                           11                             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 18(11P11.2) MUTATED    79   1   1   0   3
  DEL PEAK 18(11P11.2) WILD-TYPE 173   3   1   2   2
D41V8, multiclass
     clus
vv    DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE
  M0                            79                            173
  M1                             1                              3
  M1A                            1                              1
  M1B                            0                              2
  M1C                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                                cls
clus                              0  1
  DEL PEAK 18(11P11.2) MUTATED   32 28
  DEL PEAK 18(11P11.2) WILD-TYPE 72 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11P11.2) MUTATED     32   28
  DEL PEAK 18(11P11.2) WILD-TYPE   72   44
     clus
vv    DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE
  NO                            32                             72
  YES                           28                             44
[1] 2 2
[1] FALSE
D41V10, binary
                                cls
clus                               0   1
  DEL PEAK 18(11P11.2) MUTATED     8  83
  DEL PEAK 18(11P11.2) WILD-TYPE  26 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11P11.2) MUTATED      8   83
  DEL PEAK 18(11P11.2) WILD-TYPE   26  164
     clus
vv    DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE
  NO                             8                             26
  YES                           83                            164
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, binary
                                cls
clus                               0   1
  DEL PEAK 18(11P11.2) MUTATED    46  45
  DEL PEAK 18(11P11.2) WILD-TYPE  62 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11P11.2) MUTATED     46   45
  DEL PEAK 18(11P11.2) WILD-TYPE   62  128
        clus
vv       DEL PEAK 18(11P11.2) MUTATED DEL PEAK 18(11P11.2) WILD-TYPE
  FEMALE                           46                             62
  MALE                             45                            128
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(11P11.2) MUTATED       2                         0    89
  DEL PEAK 18(11P11.2) WILD-TYPE     3                         1   186
D41V13, multiclass
                           clus
vv                          DEL PEAK 18(11P11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               89
                           clus
vv                          DEL PEAK 18(11P11.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                                cls
clus                               0   1
  DEL PEAK 18(11P11.2) MUTATED     0  91
  DEL PEAK 18(11P11.2) WILD-TYPE   3 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11P11.2) MUTATED      0   91
  DEL PEAK 18(11P11.2) WILD-TYPE    3  183
                        clus
vv                       DEL PEAK 18(11P11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           91
                        clus
vv                       DEL PEAK 18(11P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            183
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 19(11Q23.3) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(11Q23.3) MUTATED   74 74
  DEL PEAK 19(11Q23.3) WILD-TYPE 63 59
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                           148                            122 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                            74                             59 
$`DEL PEAK 19(11Q23.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.47        32.42       110.79        22.55        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JL 
       85.32        68.22        69.90        11.41        30.87        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF 
       56.19        64.44        15.25        46.98        61.38        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GN 
        6.31         9.34        26.37         5.39        80.22        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        1.55         6.97        23.11         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 
       13.22        14.60        48.79        35.80        39.19        44.52 
TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       25.15         7.00        17.56        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20F 
        0.00        10.55         8.12         1.35        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
        9.21         1.18         7.99        37.97        11.15         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08        27.12         9.50         8.09         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
        6.48         2.43        23.90         9.67        39.39        34.29 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2GU 
       34.92        47.21        30.08        19.43         1.15        36.33 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       98.27        47.51         9.53        63.42       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       25.08        26.99        27.16        23.05         5.56       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
        3.68        30.15        15.95        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       22.22        13.94        31.40        12.95         5.72         3.78 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
        3.52        11.11        13.45        28.60        42.84         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       36.07        17.72         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       85.74         4.90         3.58        23.80        14.24         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        7.30         3.39        19.53        11.08        30.87        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       47.38         8.65        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 
        5.23         7.36        28.73        14.20         2.27         0.20 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.13        24.85        31.33        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-QB-A6FS 
       12.16        14.70        10.65         5.79 

$`DEL PEAK 19(11Q23.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
        8.52       111.09        70.16        28.08        45.83         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP 
       21.14        88.50         7.50        36.16         6.31        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A51F 
      114.67        46.32        82.29        13.32       103.59        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       95.38        47.87         4.01        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69         4.93        22.36         6.64        19.36 
TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       14.83         0.13        13.22         0.20        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29B 
        1.12        12.20         5.13         4.31         4.34         9.90 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       38.63         8.55        12.03         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       49.22         8.94        17.98        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       33.83        30.84         5.42        13.02        34.98         8.84 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        2.70         6.18        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
      111.78        21.60        29.65       124.31        25.84        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       12.72         3.22        22.92        27.35         0.46        33.60 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G 
       18.61        38.40        76.41        25.18        11.90       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-FR-A729 
       34.88         4.21        34.68        78.44        11.80         6.71 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZC 
        5.36        64.47         3.45        11.01        15.52        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        8.22         7.17        12.89        52.08         8.81        49.15 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
       53.85         3.22        10.78         5.98         6.41         0.99 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 
        0.16         0.43         9.90         7.23        12.85        84.72 
TCGA-GN-A4U8 TCGA-OD-A75X 
       11.84        11.05 

  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                          0.00                           0.13 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                        14.420                         13.745 
[1] "0.0 - 122.7 (14.4)" "0.1 - 124.3 (13.7)"
[1] "hr=" "1.1"
D42V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(11Q23.3) MUTATED   78 75
  DEL PEAK 19(11Q23.3) WILD-TYPE 64 59
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                           153                            123 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                            75                             59 
$`DEL PEAK 19(11Q23.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.57       112.57       133.25        31.59        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JL 
      103.10       168.00        69.90        11.87        48.76       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF 
       56.19        66.08        58.06        46.98        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GN 
       13.87         9.34        39.75        21.47       161.85       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        6.41         3.25         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F3 
       48.89        36.03       194.83       107.34        53.92        10.49 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
      215.44        13.87        10.16        45.11        35.01         3.55 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       27.22        94.98        14.70       109.64        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
       13.55        63.35        47.84        13.97        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       44.35        18.61        37.35        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       25.87        24.43        39.29        47.54        67.43       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 
      208.04        48.72        89.33        14.30        94.82       129.27 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       61.51        47.28        96.23       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD 
      248.65       136.47        41.59        53.26       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       54.51        23.47        36.95        64.08        34.32        53.19 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
      101.79        31.40        13.94         9.17        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
       26.37       131.51        61.05        44.05        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        4.90        15.16       202.65        20.91         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       48.85        40.27        15.45        32.75        47.38       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      133.55        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       66.67        28.73       174.84        77.88         0.20        47.54 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-QB-A6FS 
       39.58        12.62         6.67 

$`DEL PEAK 19(11Q23.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
       16.67       112.04        71.80        28.08        90.90        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP 
       23.77       115.53       113.52        42.08        12.10        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A51F 
      130.72        46.32       166.52        60.23       103.59        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
      110.93       137.92        11.34       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93        61.18        65.92        23.44        68.09        28.60 
TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       15.68        17.85        52.01         6.35        12.20        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        33.73        26.89        68.15         4.96       151.27 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X 
       80.61        39.62        72.07        56.42       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL 
       46.82       102.90        58.75       314.56        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        90.97       101.95        13.91        55.59        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       21.67        28.83        19.76       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AC 
      204.66       144.76        43.23       103.56       124.31        25.84 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JD TCGA-EE-A3JE 
       13.81       138.81       172.18       127.20        27.35        33.40 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E 
      148.08        35.44        50.76        77.75        98.40        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A1A1 TCGA-ER-A2NC 
      268.93       152.35         6.44       162.08        79.99        43.82 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 
      210.08         7.00       216.92        48.59       228.59        28.08 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
      357.37        53.52         9.70        23.93        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
      148.80        77.82        50.14        12.43        26.73        49.45 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       22.92         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A265 TCGA-GN-A4U8 TCGA-OD-A75X 
       84.72        46.36       294.77 

  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                          0.20                           0.16 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                        345.96                         357.37 
  DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE 
                         47.38                          50.76 
[1] "0.2 - 346.0 (47.4)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1.1"
D42V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 19(11Q23.3) MUTATED                   25             4
  DEL PEAK 19(11Q23.3) WILD-TYPE                 12             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 19(11Q23.3) MUTATED                                          30
  DEL PEAK 19(11Q23.3) WILD-TYPE                                        30
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 19(11Q23.3) MUTATED                    94
  DEL PEAK 19(11Q23.3) WILD-TYPE                  85
D42V4, multiclass
                                           clus
vv                                          DEL PEAK 19(11Q23.3) MUTATED
  DISTANT METASTASIS                                                  25
  PRIMARY TUMOR                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           30
  REGIONAL LYMPH NODE                                                 94
                                           clus
vv                                          DEL PEAK 19(11Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                    12
  PRIMARY TUMOR                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             30
  REGIONAL LYMPH NODE                                                   85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 19(11Q23.3) MUTATED             5       2      14        8       13
  DEL PEAK 19(11Q23.3) WILD-TYPE           5       4       9        2       12
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 19(11Q23.3) MUTATED          7         2         7         5
  DEL PEAK 19(11Q23.3) WILD-TYPE       10         8         7         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 19(11Q23.3) MUTATED          17         10         13         27
  DEL PEAK 19(11Q23.3) WILD-TYPE        15          4         10         21
                                vv
clus                             STAGE IV
  DEL PEAK 19(11Q23.3) MUTATED          7
  DEL PEAK 19(11Q23.3) WILD-TYPE        5
D42V5, multiclass
             clus
vv            DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  I OR II NOS                            5                              5
  STAGE 0                                2                              4
  STAGE I                               14                              9
  STAGE IA                               8                              2
  STAGE IB                              13                             12
  STAGE II                               7                             10
  STAGE IIA                              2                              8
  STAGE IIB                              7                              7
  STAGE IIC                              5                              5
  STAGE III                             17                             15
  STAGE IIIA                            10                              4
  STAGE IIIB                            13                             10
  STAGE IIIC                            27                             21
  STAGE IV                               7                              5
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 19(11Q23.3) MUTATED      33 30 30 30
  DEL PEAK 19(11Q23.3) WILD-TYPE    20 30 25 27
D42V6, multiclass
       clus
vv      DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  T0+T1                           33                             20
  T2                              30                             30
  T3                              30                             25
  T4                              30                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 19(11Q23.3) MUTATED   73 32 16 20
  DEL PEAK 19(11Q23.3) WILD-TYPE 68 19 16 17
D42V7, multiclass
    clus
vv   DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  N0                           73                             68
  N1                           32                             19
  N2                           16                             16
  N3                           20                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 19(11Q23.3) MUTATED   134   2   1   1   4
  DEL PEAK 19(11Q23.3) WILD-TYPE 118   2   1   1   1
D42V8, multiclass
     clus
vv    DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  M0                           134                            118
  M1                             2                              2
  M1A                            1                              1
  M1B                            1                              1
  M1C                            4                              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                                cls
clus                              0  1
  DEL PEAK 19(11Q23.3) MUTATED   60 42
  DEL PEAK 19(11Q23.3) WILD-TYPE 44 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.3) MUTATED     60   42
  DEL PEAK 19(11Q23.3) WILD-TYPE   44   30
     clus
vv    DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  NO                            60                             44
  YES                           42                             30
[1] 2 2
[1] FALSE
D42V10, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.3) MUTATED    18 136
  DEL PEAK 19(11Q23.3) WILD-TYPE  16 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.3) MUTATED     18  136
  DEL PEAK 19(11Q23.3) WILD-TYPE   16  111
     clus
vv    DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  NO                            18                             16
  YES                          136                            111
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, binary
                                cls
clus                              0  1
  DEL PEAK 19(11Q23.3) MUTATED   65 89
  DEL PEAK 19(11Q23.3) WILD-TYPE 43 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.3) MUTATED     65   89
  DEL PEAK 19(11Q23.3) WILD-TYPE   43   84
        clus
vv       DEL PEAK 19(11Q23.3) MUTATED DEL PEAK 19(11Q23.3) WILD-TYPE
  FEMALE                           65                             43
  MALE                             89                             84
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(11Q23.3) MUTATED       3                         1   150
  DEL PEAK 19(11Q23.3) WILD-TYPE     2                         0   125
D42V13, multiclass
                           clus
vv                          DEL PEAK 19(11Q23.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              150
                           clus
vv                          DEL PEAK 19(11Q23.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q23.3) MUTATED     1 150
  DEL PEAK 19(11Q23.3) WILD-TYPE   2 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q23.3) MUTATED      1  150
  DEL PEAK 19(11Q23.3) WILD-TYPE    2  124
                        clus
vv                       DEL PEAK 19(11Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          150
                        clus
vv                       DEL PEAK 19(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            124
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 20(12Q23.3) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(12Q23.3) MUTATED    35  30
  DEL PEAK 20(12Q23.3) WILD-TYPE 102 103
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                            65                            205 
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                            30                            103 
$`DEL PEAK 20(12Q23.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J7 TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CC 
       16.47        85.32        92.42        56.19        15.25        61.38 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A6EA 
        5.39        41.10         8.84        47.87         1.55        11.31 
TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29D 
       13.22        39.19         0.00        36.07         4.34        11.15 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GH 
        8.55         8.09         9.99         8.09        23.90        47.21 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP 
        5.42         1.15        36.33        44.25       111.78        26.99 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
       27.16         5.56       124.31         3.68        30.15         3.22 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
       21.60        22.22         0.46        33.60        31.40        12.95 
TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL 
        5.72        11.90        36.07         1.87         1.51         1.71 
TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZM 
       85.74         3.45        15.52         7.30        30.87        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
        8.65        40.64         3.22        28.73        10.78         5.98 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A268 TCGA-OD-A75X 
        0.99         0.13        16.24        15.42        11.05 

$`DEL PEAK 20(12Q23.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        81.24        10.29         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       36.16         6.31        64.44        45.11       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
      103.59        26.37        80.22        42.71        15.09        17.72 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU 
       20.48        13.94        95.38        52.01         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01         2.89         9.90        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       17.56        14.83        13.15         0.20         0.13         0.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.22         0.20        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F 
        1.12         1.35        12.20         5.13         4.31         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        9.21         1.18         7.99         9.90        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        4.41         1.08        27.12         9.50        12.03         8.84 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        6.48         2.43         8.68        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
        8.94        39.39        34.29        17.98        34.92        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51         9.53        29.46         7.96        14.56        63.42 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      111.91        56.02        25.08        21.60        29.65        23.05 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
      122.73        25.84        13.81        15.95        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 
       21.60        16.14        27.35        13.94        18.61        38.40 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       76.41        25.18         3.78         3.52        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG 
        9.57        17.72        78.44        11.80        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P 
       11.74         9.04         6.58        22.49        18.41         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        6.71         3.58         5.36        64.47        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       14.24         7.33         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
       11.08         7.17        12.92        12.89        52.08         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       49.15         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
        7.36        14.20         6.41         2.27         0.20         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        10.13        12.16        14.70        11.84        10.65 
TCGA-QB-A6FS 
        5.79 

  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                        124.31                         122.73 
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                         13.22                          14.20 
[1] "0.0 - 124.3 (13.2)" "0.0 - 122.7 (14.2)"
[1] "hr=" "1"  
D43V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(12Q23.3) MUTATED    37  30
  DEL PEAK 20(12Q23.3) WILD-TYPE 105 104
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                            67                            209 
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                            30                            104 
$`DEL PEAK 20(12Q23.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J7 TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CC 
       16.57       103.10       171.58        56.19        58.06        86.93 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A148 
       21.47       131.90        10.03       137.92       166.19       151.53 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A20B 
       25.18        66.25       194.83        35.01         3.55       109.64 
TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X 
      151.27        13.97        72.07        37.35        55.92        17.92 
TCGA-EE-A2A2 TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG 
       24.43       208.04        13.91        14.30        94.82       103.20 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD 
      144.76       248.65       136.47        53.26       124.31         3.68 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI 
       54.51       172.18        64.08        53.19        33.40       148.08 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A2ND 
       31.40        13.94         9.17        13.02        37.25        23.34 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA 
       20.15        33.21       174.21        48.59        28.08        27.72 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 
       32.75       101.26       133.55        53.16        50.14        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A268 
       12.43        26.73        22.92        47.54        64.44        62.79 
TCGA-OD-A75X 
      294.77 

$`DEL PEAK 20(12Q23.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74        43.43        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       42.08        12.10        66.08        45.11       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
      103.59        39.75       161.85        43.69        40.14        18.38 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU 
       51.68        15.06       110.93       135.75         7.43       125.19 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       22.95        48.89        36.03       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.16        17.85        45.11        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       26.89        68.15         4.96        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       63.35        80.61        47.84        39.62        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       44.35        18.61        56.42        14.47       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      171.55        46.82       102.90        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       135.95        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48        90.97       101.95        55.59        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      103.27        16.96       204.66        96.23       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       47.54        43.23       103.56        41.59       122.73        25.84 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        23.47       138.81       127.20        36.95        34.32 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       27.35       101.79        35.44        50.76        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
      131.51        61.05        44.05       162.08        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       79.99        43.82        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       80.32        46.98        92.98         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        7.00       216.92       228.59       202.65        20.91         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       47.38        23.93        74.73        11.41       148.80        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       49.48        27.09        27.02        77.82        66.67       174.84 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45        77.88         0.20         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       32.48        39.58        46.36        12.62         6.67 

  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                          3.55                           0.16 
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                        294.77                         357.37 
  DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE 
                         53.19                          47.28 
[1] "3.5 - 294.8 (53.2)" "0.2 - 357.4 (47.3)"
[1] "hr=" "1.2"
D43V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 20(12Q23.3) MUTATED                    9             2
  DEL PEAK 20(12Q23.3) WILD-TYPE                 28             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 20(12Q23.3) MUTATED                                          18
  DEL PEAK 20(12Q23.3) WILD-TYPE                                        42
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 20(12Q23.3) MUTATED                    38
  DEL PEAK 20(12Q23.3) WILD-TYPE                 141
D43V4, multiclass
                                           clus
vv                                          DEL PEAK 20(12Q23.3) MUTATED
  DISTANT METASTASIS                                                   9
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           18
  REGIONAL LYMPH NODE                                                 38
                                           clus
vv                                          DEL PEAK 20(12Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                    28
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             42
  REGIONAL LYMPH NODE                                                  141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 20(12Q23.3) MUTATED             3       2       7        3        6
  DEL PEAK 20(12Q23.3) WILD-TYPE           7       4      16        7       19
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 20(12Q23.3) MUTATED          5         1         3         2
  DEL PEAK 20(12Q23.3) WILD-TYPE       12         9        11         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 20(12Q23.3) MUTATED          12          3          5          9
  DEL PEAK 20(12Q23.3) WILD-TYPE        20         11         18         39
                                vv
clus                             STAGE IV
  DEL PEAK 20(12Q23.3) MUTATED          3
  DEL PEAK 20(12Q23.3) WILD-TYPE        9
D43V5, multiclass
             clus
vv            DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE
  I OR II NOS                            3                              7
  STAGE 0                                2                              4
  STAGE I                                7                             16
  STAGE IA                               3                              7
  STAGE IB                               6                             19
  STAGE II                               5                             12
  STAGE IIA                              1                              9
  STAGE IIB                              3                             11
  STAGE IIC                              2                              8
  STAGE III                             12                             20
  STAGE IIIA                             3                             11
  STAGE IIIB                             5                             18
  STAGE IIIC                             9                             39
  STAGE IV                               3                              9
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 20(12Q23.3) MUTATED      13 16 12 16
  DEL PEAK 20(12Q23.3) WILD-TYPE    40 44 43 41
D43V6, multiclass
       clus
vv      DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE
  T0+T1                           13                             40
  T2                              16                             44
  T3                              12                             43
  T4                              16                             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 20(12Q23.3) MUTATED    35  16   6   8
  DEL PEAK 20(12Q23.3) WILD-TYPE 106  35  26  29
D43V7, multiclass
    clus
vv   DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE
  N0                           35                            106
  N1                           16                             35
  N2                            6                             26
  N3                            8                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 20(12Q23.3) MUTATED    62   0   1   1   2
  DEL PEAK 20(12Q23.3) WILD-TYPE 190   4   1   1   3
D43V8, multiclass
     clus
vv    DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE
  M0                            62                            190
  M1                             0                              4
  M1A                            1                              1
  M1B                            1                              1
  M1C                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                                cls
clus                              0  1
  DEL PEAK 20(12Q23.3) MUTATED   24 17
  DEL PEAK 20(12Q23.3) WILD-TYPE 80 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12Q23.3) MUTATED     24   17
  DEL PEAK 20(12Q23.3) WILD-TYPE   80   55
     clus
vv    DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE
  NO                            24                             80
  YES                           17                             55
[1] 2 2
[1] FALSE
D43V10, binary
                                cls
clus                               0   1
  DEL PEAK 20(12Q23.3) MUTATED     7  61
  DEL PEAK 20(12Q23.3) WILD-TYPE  27 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12Q23.3) MUTATED      7   61
  DEL PEAK 20(12Q23.3) WILD-TYPE   27  186
     clus
vv    DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE
  NO                             7                             27
  YES                           61                            186
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, binary
                                cls
clus                               0   1
  DEL PEAK 20(12Q23.3) MUTATED    31  37
  DEL PEAK 20(12Q23.3) WILD-TYPE  77 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12Q23.3) MUTATED     31   37
  DEL PEAK 20(12Q23.3) WILD-TYPE   77  136
        clus
vv       DEL PEAK 20(12Q23.3) MUTATED DEL PEAK 20(12Q23.3) WILD-TYPE
  FEMALE                           31                             77
  MALE                             37                            136
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(12Q23.3) MUTATED       0                         0    68
  DEL PEAK 20(12Q23.3) WILD-TYPE     5                         1   207
D43V13, multiclass
                           clus
vv                          DEL PEAK 20(12Q23.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               68
                           clus
vv                          DEL PEAK 20(12Q23.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                                cls
clus                               0   1
  DEL PEAK 20(12Q23.3) MUTATED     0  68
  DEL PEAK 20(12Q23.3) WILD-TYPE   3 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12Q23.3) MUTATED      0   68
  DEL PEAK 20(12Q23.3) WILD-TYPE    3  206
                        clus
vv                       DEL PEAK 20(12Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       DEL PEAK 20(12Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            206
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 21(13Q12.11) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 21(13Q12.11) MUTATED    34  28
  DEL PEAK 21(13Q12.11) WILD-TYPE 103 105
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             62                             208 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             28                             105 
$`DEL PEAK 21(13Q12.11) MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL 
       28.08        10.29        85.32        88.50        69.90        92.42 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
      103.59        26.37        17.72        20.48        95.38        52.01 
TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I4 
        1.55         2.89        11.31        48.79        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A20I 
       44.52        25.15         6.64        13.22         1.12         1.18 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        11.15        38.63         1.08        27.12         9.50 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI 
        8.09         8.84         8.68         8.94        34.92        30.08 
TCGA-EE-A2GJ TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A2MS 
       19.43         8.84        44.25         7.96        29.65        27.16 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JH TCGA-ER-A193 
        5.56       122.73        30.15        21.60        13.94        31.40 
TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A3YN 
       25.18        34.88         1.87         1.51        12.62        18.41 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZY TCGA-FS-A4F4 
        5.36        64.47         7.30        30.87         0.82         7.36 
TCGA-GN-A266 TCGA-GN-A26D 
       10.13        14.70 

$`DEL PEAK 21(13Q12.11) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       22.55        45.83        81.24         8.38        21.14        68.22 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       11.41        30.87         7.50        36.16         6.31        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
        5.39        80.22        42.71        15.09        41.10         8.84 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 
       13.94        47.87         6.97        23.11         4.01         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        14.60        35.80        51.12        10.03        39.19 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       36.69         4.93        22.36        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       14.83        13.15         0.20         0.13         0.00         0.00 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
        0.20        11.57        10.55         6.31         8.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
        9.21         7.99         9.90         8.55         4.41        12.03 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH 
       23.90         9.67        39.39        34.29        17.98        47.21 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ 
        6.18        47.51         9.53        29.46        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       23.05       124.31        25.84         3.68        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35         0.46        33.60        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        5.72        76.41         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      114.15         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
        9.57        36.07        17.72        78.44        11.80        13.08 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       11.74         9.04         6.58        22.49         1.71        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.90         6.71         3.58         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       14.24        15.52         7.33         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       19.53        11.08         7.17        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         5.23        53.85         3.22        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                           0.82                            0.00 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                         122.73                          124.31 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                         18.065                          13.630 
[1] "0.8 - 122.7 (18.1)" "0.0 - 124.3 (13.6)"
[1] "hr=" "1.2"
D44V2, survival
                                 sevent
clus2                               0   1
  DEL PEAK 21(13Q12.11) MUTATED    37  28
  DEL PEAK 21(13Q12.11) WILD-TYPE 105 106
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             65                             211 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             28                             106 
$`DEL PEAK 21(13Q12.11) MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL 
       28.08        43.43       103.10       115.53        69.90       171.58 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
      103.59        39.75        18.38        51.68       110.93       135.75 
TCGA-D3-A5GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV 
      166.19       151.53        54.67         3.25        25.18        48.89 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A5UL 
      176.55        35.93       107.34        53.92        68.09         3.55 
TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       52.01        33.73        13.55        47.84        13.97        39.62 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
        2.60        44.35        18.61        37.35        14.47       171.55 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2M5 TCGA-EE-A2MG 
       58.75       135.95        48.72        89.33        21.67       103.20 
TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE 
       16.96       103.56       136.47        53.26       122.73        54.51 
TCGA-EE-A3J5 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A2ND 
       36.95       101.79        31.40        98.40       152.35        23.34 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1ZA 
       20.15        31.27        92.98         7.00       216.92        27.72 
TCGA-FS-A1ZH TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-GN-A266 TCGA-GN-A26D 
       32.75        27.09        66.67        10.13        39.58 

$`DEL PEAK 21(13Q12.11) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       31.59        90.90        95.74        65.49        23.77       168.00 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       11.87        48.76       113.52        42.08        12.10        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       21.47       161.85        43.69        40.14       131.90        10.03 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX 
       15.06       137.92         7.43       125.19         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
       11.34         9.90        66.25        22.95        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
       20.38       194.83        61.18        65.92        23.44        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       45.11        35.01         6.35        12.20        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
      109.64       151.27        78.87       168.26        63.35        80.61 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       72.07        32.19        56.42        55.92       345.96        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
       17.92        46.82       102.90        24.43        39.29        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       67.43       314.56       208.04        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.27       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
       47.54       248.65        43.23        41.59       124.31        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       64.08        34.32        53.19        27.35        33.40       148.08 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       35.44        13.94        50.76         9.17        77.75        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02        26.37       268.93         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       79.99        43.82        16.37        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       46.98        33.21       174.21         4.90       210.08        15.16 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        49.48        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       64.44        62.79        32.48        46.36        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                           2.60                            0.16 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                         216.92                          357.37 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                          48.89                           47.54 
[1] "2.6 - 216.9 (48.9)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.1"
D44V3, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 21(13Q12.11) MUTATED                    6             1
  DEL PEAK 21(13Q12.11) WILD-TYPE                 31             3
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 21(13Q12.11) MUTATED                                          14
  DEL PEAK 21(13Q12.11) WILD-TYPE                                        46
                                 vv
clus                              REGIONAL LYMPH NODE
  DEL PEAK 21(13Q12.11) MUTATED                    44
  DEL PEAK 21(13Q12.11) WILD-TYPE                 135
D44V4, multiclass
                                           clus
vv                                          DEL PEAK 21(13Q12.11) MUTATED
  DISTANT METASTASIS                                                    6
  PRIMARY TUMOR                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            14
  REGIONAL LYMPH NODE                                                  44
                                           clus
vv                                          DEL PEAK 21(13Q12.11) WILD-TYPE
  DISTANT METASTASIS                                                     31
  PRIMARY TUMOR                                                           3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                              46
  REGIONAL LYMPH NODE                                                   135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 21(13Q12.11) MUTATED             2       2       5        5        6
  DEL PEAK 21(13Q12.11) WILD-TYPE           8       4      18        5       19
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 21(13Q12.11) MUTATED          2         2         4         2
  DEL PEAK 21(13Q12.11) WILD-TYPE       15         8        10         8
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 21(13Q12.11) MUTATED           7          2          6         11
  DEL PEAK 21(13Q12.11) WILD-TYPE        25         12         17         37
                                 vv
clus                              STAGE IV
  DEL PEAK 21(13Q12.11) MUTATED          4
  DEL PEAK 21(13Q12.11) WILD-TYPE        8
D44V5, multiclass
             clus
vv            DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE
  I OR II NOS                             2                               8
  STAGE 0                                 2                               4
  STAGE I                                 5                              18
  STAGE IA                                5                               5
  STAGE IB                                6                              19
  STAGE II                                2                              15
  STAGE IIA                               2                               8
  STAGE IIB                               4                              10
  STAGE IIC                               2                               8
  STAGE III                               7                              25
  STAGE IIIA                              2                              12
  STAGE IIIB                              6                              17
  STAGE IIIC                             11                              37
  STAGE IV                                4                               8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 21(13Q12.11) MUTATED      15 11 18  9
  DEL PEAK 21(13Q12.11) WILD-TYPE    38 49 37 48
D44V6, multiclass
       clus
vv      DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE
  T0+T1                            15                              38
  T2                               11                              49
  T3                               18                              37
  T4                                9                              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 21(13Q12.11) MUTATED    34  11  10   8
  DEL PEAK 21(13Q12.11) WILD-TYPE 107  40  22  29
D44V7, multiclass
    clus
vv   DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE
  N0                            34                             107
  N1                            11                              40
  N2                            10                              22
  N3                             8                              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B M1C
  DEL PEAK 21(13Q12.11) MUTATED    58   0   0   2   3
  DEL PEAK 21(13Q12.11) WILD-TYPE 194   4   2   0   2
D44V8, multiclass
     clus
vv    DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE
  M0                             58                             194
  M1                              0                               4
  M1A                             0                               2
  M1B                             2                               0
  M1C                             3                               2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                                 cls
clus                               0  1
  DEL PEAK 21(13Q12.11) MUTATED   28 18
  DEL PEAK 21(13Q12.11) WILD-TYPE 76 54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(13Q12.11) MUTATED     28   18
  DEL PEAK 21(13Q12.11) WILD-TYPE   76   54
     clus
vv    DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE
  NO                             28                              76
  YES                            18                              54
[1] 2 2
[1] FALSE
D44V10, binary
                                 cls
clus                                0   1
  DEL PEAK 21(13Q12.11) MUTATED     6  59
  DEL PEAK 21(13Q12.11) WILD-TYPE  28 188
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(13Q12.11) MUTATED      6   59
  DEL PEAK 21(13Q12.11) WILD-TYPE   28  188
     clus
vv    DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE
  NO                              6                              28
  YES                            59                             188
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, binary
                                 cls
clus                                0   1
  DEL PEAK 21(13Q12.11) MUTATED    20  45
  DEL PEAK 21(13Q12.11) WILD-TYPE  88 128
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(13Q12.11) MUTATED     20   45
  DEL PEAK 21(13Q12.11) WILD-TYPE   88  128
        clus
vv       DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE
  FEMALE                            20                              88
  MALE                              45                             128
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(13Q12.11) MUTATED       0                         0    65
  DEL PEAK 21(13Q12.11) WILD-TYPE     5                         1   210
D44V13, multiclass
                           clus
vv                          DEL PEAK 21(13Q12.11) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                65
                           clus
vv                          DEL PEAK 21(13Q12.11) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                 210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                                 cls
clus                                0   1
  DEL PEAK 21(13Q12.11) MUTATED     1  63
  DEL PEAK 21(13Q12.11) WILD-TYPE   2 211
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(13Q12.11) MUTATED      1   63
  DEL PEAK 21(13Q12.11) WILD-TYPE    2  211
                        clus
vv                       DEL PEAK 21(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            63
                        clus
vv                       DEL PEAK 21(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             211
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 22(13Q34) MUTATION ANALYSIS
D45V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 22(13Q34) MUTATED    32  27
  DEL PEAK 22(13Q34) WILD-TYPE 105 106
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                          59                          211 
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                          27                          106 
$`DEL PEAK 22(13Q34) MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC 
       28.08        22.55        85.32         8.38        88.50        69.90 
TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GL TCGA-D3-A5GN 
       92.42        46.98       103.59        26.37        95.38        52.01 
TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 
        1.55         2.89        11.31        48.79        35.80        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A5UN TCGA-EE-A181 
        9.99        44.52        25.15         6.64        13.22         1.12 
TCGA-EE-A184 TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29Q 
        5.13         1.18        11.15        38.63         9.50         8.09 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
        6.48         8.94        34.92        30.08        19.43        28.31 
TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
        8.84        44.25         7.96        29.65        27.16         5.56 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JH TCGA-ER-A193 
      122.73        30.15        12.72        21.60        13.94        31.40 
TCGA-ER-A19Q TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FS-A1ZA TCGA-FS-A1ZH 
        9.57        12.62        18.41         5.36         7.30        30.87 
TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-GN-A266 TCGA-GN-A26D 
       12.92         7.36        10.78        10.13        14.70 

$`DEL PEAK 22(13Q34) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD 
       45.83        81.24        10.29        21.14        68.22        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87         7.50        36.16         6.31        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         6.31         9.34         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 
       13.94        47.87         6.97        23.11         4.01         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 
       13.22        14.60        51.12        10.03        39.19        36.69 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
        4.93        22.36        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 
       13.15         0.20         0.13         0.00         0.00         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       11.57        10.55         6.31         8.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        4.31        36.07         4.34         5.13         9.21         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        9.90        37.97         8.55         4.41         1.08        27.12 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       12.03         8.84         9.99         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22        23.90         9.67        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       17.98        47.21        16.01        35.54        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
        5.42         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MI 
        2.70         6.18        47.51         9.53        29.46        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       21.60        23.05       124.31        25.84         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       15.95         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35         0.46        33.60        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84        34.68        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.87         1.51        13.08        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       22.49         1.71        85.74         4.90         6.71         3.58 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         3.22        28.73        14.20         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       16.24        15.42        12.16        11.84        10.65        11.05 
TCGA-QB-A6FS 
        5.79 

  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                        1.12                         0.00 
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                      122.73                       124.31 
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                       14.70                        13.94 
[1] "1.1 - 122.7 (14.7)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1.2"
D45V2, survival
                              sevent
clus2                            0   1
  DEL PEAK 22(13Q34) MUTATED    35  27
  DEL PEAK 22(13Q34) WILD-TYPE 107 107
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                          62                          214 
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                          27                          107 
$`DEL PEAK 22(13Q34) MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC 
       28.08        31.59       103.10        65.49       115.53        69.90 
TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GL TCGA-D3-A5GN 
      171.58        46.98       103.59        39.75       110.93       135.75 
TCGA-D3-A5GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV 
      166.19       151.53        54.67         3.25        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC 
       36.03       176.55        35.93       107.34        53.92        68.09 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20I TCGA-EE-A29D 
        3.55        52.01        33.73        68.15        13.55        13.97 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE 
       39.62        18.61        37.35       345.96        58.75       135.95 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH 
       48.72        89.33        75.48        21.67       103.20        16.96 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AH 
      103.56       136.47        53.26       122.73        54.51       138.81 
TCGA-EE-A3J5 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19Q TCGA-ER-A2NG TCGA-FR-A3YN 
       36.95       101.79        31.40        50.89        31.27        92.98 
TCGA-FR-A7U9 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-FS-A4F9 
        7.00        27.72        32.75        47.38        66.67        12.43 
TCGA-GN-A266 TCGA-GN-A26D 
       10.13        39.58 

$`DEL PEAK 22(13Q34) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD 
       90.90        95.74        43.43        23.77       168.00        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76       113.52        42.08        12.10        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53        13.87         9.34        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX 
       15.06       137.92         7.43       125.19         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
       11.34         9.90        66.25        22.95       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
      194.83        61.18        65.92        23.44        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        45.11 
TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       35.01         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       94.98        14.70        26.89         4.96       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
       78.87       168.26        63.35        80.61        47.84        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       32.19         2.60        44.35        56.42        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK 
       39.29        47.54        67.43       314.56       208.04        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       47.28       103.27       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA 
      167.90        47.54       248.65        43.23        41.59       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84         3.68        13.81        23.47       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       64.08        34.32        53.19        27.35        33.40       148.08 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
        6.44       131.51        61.05        44.05       162.08        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        33.21       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        4.90       210.08        15.16       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        20.91        28.08         7.79        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM 
       53.52        40.27        15.45         9.70        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
      174.84        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                        3.25                         0.16 
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                      345.96                       357.37 
  DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE 
                      52.635                       47.130 
[1] "3.2 - 346.0 (52.6)" "0.2 - 357.4 (47.1)"
[1] "hr=" "1.2"
D45V3, continuous
                              vv
clus                           DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 22(13Q34) MUTATED                    4             1
  DEL PEAK 22(13Q34) WILD-TYPE                 33             3
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 22(13Q34) MUTATED                                          13
  DEL PEAK 22(13Q34) WILD-TYPE                                        47
                              vv
clus                           REGIONAL LYMPH NODE
  DEL PEAK 22(13Q34) MUTATED                    44
  DEL PEAK 22(13Q34) WILD-TYPE                 135
D45V4, multiclass
                                           clus
vv                                          DEL PEAK 22(13Q34) MUTATED
  DISTANT METASTASIS                                                 4
  PRIMARY TUMOR                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                         13
  REGIONAL LYMPH NODE                                               44
                                           clus
vv                                          DEL PEAK 22(13Q34) WILD-TYPE
  DISTANT METASTASIS                                                  33
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           47
  REGIONAL LYMPH NODE                                                135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 22(13Q34) MUTATED             2       0       6        5        5
  DEL PEAK 22(13Q34) WILD-TYPE           8       6      17        5       20
                              vv
clus                           STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 22(13Q34) MUTATED          3         1         2         3         8
  DEL PEAK 22(13Q34) WILD-TYPE       14         9        12         7        24
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 22(13Q34) MUTATED            2          7          9        4
  DEL PEAK 22(13Q34) WILD-TYPE         12         16         39        8
D45V5, multiclass
             clus
vv            DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE
  I OR II NOS                          2                            8
  STAGE 0                              0                            6
  STAGE I                              6                           17
  STAGE IA                             5                            5
  STAGE IB                             5                           20
  STAGE II                             3                           14
  STAGE IIA                            1                            9
  STAGE IIB                            2                           12
  STAGE IIC                            3                            7
  STAGE III                            8                           24
  STAGE IIIA                           2                           12
  STAGE IIIB                           7                           16
  STAGE IIIC                           9                           39
  STAGE IV                             4                            8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 22(13Q34) MUTATED      15 12 15 11
  DEL PEAK 22(13Q34) WILD-TYPE    38 48 40 46
D45V6, multiclass
       clus
vv      DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE
  T0+T1                         15                           38
  T2                            12                           48
  T3                            15                           40
  T4                            11                           46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  DEL PEAK 22(13Q34) MUTATED    30  12  10   7
  DEL PEAK 22(13Q34) WILD-TYPE 111  39  22  30
D45V7, multiclass
    clus
vv   DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE
  N0                         30                          111
  N1                         12                           39
  N2                         10                           22
  N3                          7                           30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B M1C
  DEL PEAK 22(13Q34) MUTATED    55   0   0   2   3
  DEL PEAK 22(13Q34) WILD-TYPE 197   4   2   0   2
D45V8, multiclass
     clus
vv    DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE
  M0                          55                          197
  M1                           0                            4
  M1A                          0                            2
  M1B                          2                            0
  M1C                          3                            2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                              cls
clus                            0  1
  DEL PEAK 22(13Q34) MUTATED   29 17
  DEL PEAK 22(13Q34) WILD-TYPE 75 55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(13Q34) MUTATED     29   17
  DEL PEAK 22(13Q34) WILD-TYPE   75   55
     clus
vv    DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE
  NO                          29                           75
  YES                         17                           55
[1] 2 2
[1] FALSE
D45V10, binary
                              cls
clus                             0   1
  DEL PEAK 22(13Q34) MUTATED     7  55
  DEL PEAK 22(13Q34) WILD-TYPE  27 192
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(13Q34) MUTATED      7   55
  DEL PEAK 22(13Q34) WILD-TYPE   27  192
     clus
vv    DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE
  NO                           7                           27
  YES                         55                          192
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, binary
                              cls
clus                             0   1
  DEL PEAK 22(13Q34) MUTATED    23  39
  DEL PEAK 22(13Q34) WILD-TYPE  85 134
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(13Q34) MUTATED     23   39
  DEL PEAK 22(13Q34) WILD-TYPE   85  134
        clus
vv       DEL PEAK 22(13Q34) MUTATED DEL PEAK 22(13Q34) WILD-TYPE
  FEMALE                         23                           85
  MALE                           39                          134
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(13Q34) MUTATED       0                         0    62
  DEL PEAK 22(13Q34) WILD-TYPE     5                         1   213
D45V13, multiclass
                           clus
vv                          DEL PEAK 22(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             62
                           clus
vv                          DEL PEAK 22(13Q34) WILD-TYPE
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                              cls
clus                             0   1
  DEL PEAK 22(13Q34) MUTATED     0  61
  DEL PEAK 22(13Q34) WILD-TYPE   3 213
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(13Q34) MUTATED      0   61
  DEL PEAK 22(13Q34) WILD-TYPE    3  213
                        clus
vv                       DEL PEAK 22(13Q34) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         61
                        clus
vv                       DEL PEAK 22(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          213
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 23(14Q23.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(14Q23.3) MUTATED   46 47
  DEL PEAK 23(14Q23.3) WILD-TYPE 91 86
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                            93                            177 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                            47                             86 
$`DEL PEAK 23(14Q23.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A2JN 
       16.47       111.09        10.29        88.50        30.87        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV 
       64.44        45.11        61.38        13.32       103.59         5.39 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A6EA 
       41.10         8.84        52.01        47.87         1.55        11.31 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
       48.79        51.12        39.19        44.52        25.15        17.56 
TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29P 
        0.20        10.55         1.12        37.97         8.55        12.03 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE 
        2.43         8.09        23.90         9.67         8.94        34.92 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       47.21         5.42        36.33        98.27         2.70         6.18 
TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MQ 
        9.53        44.25         7.96       111.78        25.08        21.60 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
       27.16       124.31        12.72         3.22        21.60        21.60 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
       22.22         0.46        33.60        12.95         5.72        25.18 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND 
       11.90       114.15        34.88        36.07        17.72         1.87 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        1.71        85.74         3.45        15.52         7.33         7.30 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       20.38        19.53        30.87        47.38         8.65         8.81 
TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       40.64         3.22         7.36        28.73        14.20        10.78 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        0.13         7.23        12.85        31.33        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       12.16        10.65        11.05 

$`DEL PEAK 23(14Q23.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
        8.52        32.42        70.16       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       45.83        81.24        85.32         8.38        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        11.41         7.50        36.16         6.31        92.42 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
      114.67        15.25        46.98        46.32        82.29        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        6.31         9.34        26.37        80.22        42.71        15.09 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU 
       17.72        20.48        13.94        95.38         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
        4.01         2.89         9.90        13.22        14.60        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       10.03        13.68         9.99        36.69         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
        6.64        19.36         7.00        14.83        13.15         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
        0.00         0.00        13.22         0.20        11.57         6.31 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         4.41         1.08        27.12         9.50 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
        8.09         8.84         9.99         6.48         8.68        11.31 
TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ 
       49.22        39.39        34.29        17.98        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83        30.84         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MI 
       13.02        34.98         8.84        47.51        29.46        14.56 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT 
       63.42       111.91        56.02        26.99        29.65        23.05 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 
       15.95        22.92        16.14        27.35        13.94        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       18.61        38.40        76.41         3.78         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44        11.80         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 
        9.04         6.58        22.49        18.41         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.58         5.36        64.47        11.01        23.80        14.24 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        3.39         8.22        11.08         7.17        12.92        12.89 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       52.08        49.15         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.85         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        0.16         0.43         9.90        24.85        84.72        10.13 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       14.70        11.84         5.79 

  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                        124.31                         122.73 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                         16.47                          13.45 
[1] "0.1 - 124.3 (16.5)" "0.0 - 122.7 (13.4)"
[1] "hr=" "1.1"
D46V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(14Q23.3) MUTATED   48 47
  DEL PEAK 23(14Q23.3) WILD-TYPE 94 87
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                            95                            181 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                            47                             87 
$`DEL PEAK 23(14Q23.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A2JN 
       16.57       112.04        43.43       115.53        48.76        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV 
       66.08        45.11        86.93        60.23       103.59        21.47 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A149 
      131.90        10.03       135.75       137.92       166.19        54.67 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 
       25.18        48.89       117.21       194.83       107.34        53.92 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C 
      215.44        10.16         3.55        27.22        33.73        47.84 
TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
       72.07        56.42        25.87        17.92        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 
       58.75       135.95       208.04        13.91        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.83        19.76        47.28       103.20        16.96       144.76 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 
       47.54        43.23       136.47       124.31       138.81       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 
       36.95        64.08        53.19        33.40       148.08        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S 
        9.17        98.40        13.02       268.93       152.35        37.25 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 
      148.18        23.34        33.21       174.21        48.59        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM 
        7.79        27.72       357.37        40.27        32.75       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
      133.55        11.41        53.16        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 
      174.84        12.43        47.54         7.23        14.04       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       64.44        62.79        32.48        12.62       294.77 

$`DEL PEAK 23(14Q23.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        95.74       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
      130.72        58.06        46.98        46.32       166.52        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.87         9.34        39.75       161.85        43.69        40.14 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU 
       18.38        51.68        15.06       110.93         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       66.25        22.95        36.03        20.38       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       15.68        13.87        17.85        45.11        35.01        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
        6.35        12.20        29.82         8.65        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
      168.26        13.55        63.35        80.61        13.97        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       32.19         2.60        44.35        18.61        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GB 
       55.92       345.96       171.55        46.82       102.90        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       314.56        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        90.97       101.95        14.30        55.59        44.88 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
       21.67        61.51       103.27       204.66        96.23       203.05 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      167.90       248.65       103.56        41.59        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 
       25.84         3.68        54.51        13.81        23.47       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       34.32        27.35       101.79        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       77.75        48.89        12.59        26.37         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC 
       61.05        44.05       162.08        50.89        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98        92.98         4.90       210.08        15.16         7.00 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZD 
      216.92       228.59       202.65        20.91        48.85        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS 
       15.45         9.70        47.38        23.93        74.73       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FB 
       26.56        49.48        27.09        27.02        77.82        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        22.92         0.16         2.40 
TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U8 
        9.90       120.46        84.72        10.13        39.58        46.36 
TCGA-QB-A6FS 
        6.67 

  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                          3.55                           0.16 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                        357.37                         345.96 
  DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE 
                         53.16                          46.36 
[1] "3.5 - 357.4 (53.2)" "0.2 - 346.0 (46.4)"
[1] "hr=" "1.1"
D46V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 23(14Q23.3) MUTATED                   13             1
  DEL PEAK 23(14Q23.3) WILD-TYPE                 24             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 23(14Q23.3) MUTATED                                          28
  DEL PEAK 23(14Q23.3) WILD-TYPE                                        32
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 23(14Q23.3) MUTATED                    53
  DEL PEAK 23(14Q23.3) WILD-TYPE                 126
D46V4, multiclass
                                           clus
vv                                          DEL PEAK 23(14Q23.3) MUTATED
  DISTANT METASTASIS                                                  13
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           28
  REGIONAL LYMPH NODE                                                 53
                                           clus
vv                                          DEL PEAK 23(14Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                    24
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             32
  REGIONAL LYMPH NODE                                                  126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 23(14Q23.3) MUTATED             3       0      11        3        7
  DEL PEAK 23(14Q23.3) WILD-TYPE           7       6      12        7       18
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 23(14Q23.3) MUTATED          8         1         3         4
  DEL PEAK 23(14Q23.3) WILD-TYPE        9         9        11         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 23(14Q23.3) MUTATED          13          5          8         16
  DEL PEAK 23(14Q23.3) WILD-TYPE        19          9         15         32
                                vv
clus                             STAGE IV
  DEL PEAK 23(14Q23.3) MUTATED          4
  DEL PEAK 23(14Q23.3) WILD-TYPE        8
D46V5, multiclass
             clus
vv            DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  I OR II NOS                            3                              7
  STAGE 0                                0                              6
  STAGE I                               11                             12
  STAGE IA                               3                              7
  STAGE IB                               7                             18
  STAGE II                               8                              9
  STAGE IIA                              1                              9
  STAGE IIB                              3                             11
  STAGE IIC                              4                              6
  STAGE III                             13                             19
  STAGE IIIA                             5                              9
  STAGE IIIB                             8                             15
  STAGE IIIC                            16                             32
  STAGE IV                               4                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 23(14Q23.3) MUTATED      21 24 16 20
  DEL PEAK 23(14Q23.3) WILD-TYPE    32 36 39 37
D46V6, multiclass
       clus
vv      DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  T0+T1                           21                             32
  T2                              24                             36
  T3                              16                             39
  T4                              20                             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 23(14Q23.3) MUTATED   46 22  8 13
  DEL PEAK 23(14Q23.3) WILD-TYPE 95 29 24 24
D46V7, multiclass
    clus
vv   DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  N0                           46                             95
  N1                           22                             29
  N2                            8                             24
  N3                           13                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 23(14Q23.3) MUTATED    87   0   1   0   3
  DEL PEAK 23(14Q23.3) WILD-TYPE 165   4   1   2   2
D46V8, multiclass
     clus
vv    DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  M0                            87                            165
  M1                             0                              4
  M1A                            1                              1
  M1B                            0                              2
  M1C                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                                cls
clus                              0  1
  DEL PEAK 23(14Q23.3) MUTATED   36 27
  DEL PEAK 23(14Q23.3) WILD-TYPE 68 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q23.3) MUTATED     36   27
  DEL PEAK 23(14Q23.3) WILD-TYPE   68   45
     clus
vv    DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  NO                            36                             68
  YES                           27                             45
[1] 2 2
[1] FALSE
D46V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(14Q23.3) MUTATED    11  85
  DEL PEAK 23(14Q23.3) WILD-TYPE  23 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q23.3) MUTATED     11   85
  DEL PEAK 23(14Q23.3) WILD-TYPE   23  162
     clus
vv    DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  NO                            11                             23
  YES                           85                            162
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, binary
                                cls
clus                               0   1
  DEL PEAK 23(14Q23.3) MUTATED    40  56
  DEL PEAK 23(14Q23.3) WILD-TYPE  68 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q23.3) MUTATED     40   56
  DEL PEAK 23(14Q23.3) WILD-TYPE   68  117
        clus
vv       DEL PEAK 23(14Q23.3) MUTATED DEL PEAK 23(14Q23.3) WILD-TYPE
  FEMALE                           40                             68
  MALE                             56                            117
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(14Q23.3) MUTATED       2                         0    94
  DEL PEAK 23(14Q23.3) WILD-TYPE     3                         1   181
D46V13, multiclass
                           clus
vv                          DEL PEAK 23(14Q23.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               94
                           clus
vv                          DEL PEAK 23(14Q23.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                                cls
clus                               0   1
  DEL PEAK 23(14Q23.3) MUTATED     0  94
  DEL PEAK 23(14Q23.3) WILD-TYPE   3 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q23.3) MUTATED      0   94
  DEL PEAK 23(14Q23.3) WILD-TYPE    3  180
                        clus
vv                       DEL PEAK 23(14Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       DEL PEAK 23(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            180
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 24(14Q32.2) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(14Q32.2) MUTATED   45 46
  DEL PEAK 24(14Q32.2) WILD-TYPE 92 87
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                            91                            179 
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                            46                             87 
$`DEL PEAK 24(14Q32.2) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JN 
       16.47       111.09        32.42        10.29        30.87        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV 
       64.44        45.11        61.38        13.32       103.59         5.39 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A6EA 
       41.10         8.84        52.01        47.87         1.55        11.31 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
       48.79        51.12        39.19        44.52        25.15        17.56 
TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29V 
        0.20        10.55         1.12        37.97         8.55         2.43 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
       23.90         9.67         8.94        39.39        34.92        19.43 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        5.42        36.33        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS 
        9.53        44.25         7.96       111.78        25.08        27.16 
TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
      124.31        12.72         3.22        21.60        21.60        22.22 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E 
        0.46        33.60        12.95         5.72        25.18        11.90 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL 
      114.15        34.88        36.07         1.87         1.51         1.71 
TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       85.74         3.45        15.52         7.33         7.30        20.38 
TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       19.53        30.87        47.38         8.65         8.81        40.64 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO 
        3.22        28.73        14.20        10.78         0.13         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 
       12.85        31.33        16.24        15.42        12.16        10.65 
TCGA-OD-A75X 
       11.05 

$`DEL PEAK 24(14Q32.2) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
        8.52        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       81.24        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        11.41         7.50        36.16         6.31        92.42 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
      114.67        15.25        46.98        46.32        82.29        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        6.31         9.34        26.37        80.22        42.71        15.09 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU 
       17.72        20.48        13.94        95.38         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
        4.01         2.89         9.90        13.22        14.60        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       10.03        13.68         9.99        36.69         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
        6.64        19.36         7.00        14.83        13.15         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
        0.00         0.00        13.22         0.20        11.57         6.31 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         4.41         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       12.03         8.09         8.84         9.99         6.48         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH 
        8.09        11.31        49.22        34.29        17.98        47.21 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       30.08        16.01        35.54        28.31        33.83        30.84 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2ME TCGA-EE-A2MI 
        1.15        13.02        34.98         8.84        29.46        14.56 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       63.42       111.91        56.02        26.99        21.60        29.65 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.05         5.56       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH 
       13.81        15.95        22.92        16.14        27.35        13.94 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       31.40        18.61        38.40        76.41         3.78         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.11         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG 
        9.57        17.72        78.44        11.80        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P 
       11.74         9.04         6.58        22.49        18.41         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        6.71         3.58         5.36        64.47        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       14.24         3.39         8.22        11.08         7.17        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       12.89        52.08        49.15         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        5.23        53.85         7.36         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 
        0.20         0.99         0.16         0.43         9.90        24.85 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       84.72        10.13        14.70        11.84         5.79 

  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                        124.31                         122.73 
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                         17.56                          13.22 
[1] "0.1 - 124.3 (17.6)" "0.0 - 122.7 (13.2)"
[1] "hr=" "1.1"
D47V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(14Q32.2) MUTATED   47 46
  DEL PEAK 24(14Q32.2) WILD-TYPE 95 88
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                            93                            183 
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                            46                             88 
$`DEL PEAK 24(14Q32.2) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JN 
       16.57       112.04       112.57        43.43        48.76        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV 
       66.08        45.11        86.93        60.23       103.59        21.47 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A149 
      131.90        10.03       135.75       137.92       166.19        54.67 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 
       25.18        48.89       117.21       194.83       107.34        53.92 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C 
      215.44        10.16         3.55        27.22        33.73        47.84 
TCGA-EE-A29G TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       72.07        25.87        24.43        39.29        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
      135.95        89.33        13.91        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       19.76        61.51        47.28       103.20        16.96       144.76 
TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 
       47.54       136.47       124.31       138.81       172.18        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       64.08        53.19        33.40       148.08        13.94         9.17 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND 
       98.40        13.02       268.93       152.35        37.25        23.34 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       20.15        33.21       174.21        48.59        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       27.72       357.37        40.27        32.75       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       11.41        53.16        50.14        28.73       174.84        12.43 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       47.54         7.23        14.04       117.93        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       32.48        12.62       294.77 

$`DEL PEAK 24(14Q32.2) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.67        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
      130.72        58.06        46.98        46.32       166.52        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.87         9.34        39.75       161.85        43.69        40.14 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU 
       18.38        51.68        15.06       110.93         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       66.25        22.95        36.03        20.38       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       15.68        13.87        17.85        45.11        35.01        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
        6.35        12.20        29.82         8.65        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
      168.26        13.55        63.35        80.61        13.97        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92       345.96       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
      102.90        67.43       314.56       208.04        48.72        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48        90.97       101.95        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
       44.88        21.67       103.27       204.66        96.23       203.05 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90       248.65        43.23       103.56        41.59        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      127.20        34.32        27.35       101.79        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       50.76        77.75        48.89        12.59        26.37         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
      131.51        61.05        44.05       162.08        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       79.99        43.82        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       80.32        46.98        92.98         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZB 
        7.00       216.92       228.59       202.65        20.91        48.85 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       53.52        15.45         9.70        47.38        23.93        74.73 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       66.67        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        0.16         2.40         9.90       120.46        84.72        10.13 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       39.58        46.36         6.67 

  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                          3.55                           0.16 
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                        357.37                         345.96 
  DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE 
                         50.14                          46.36 
[1] "3.5 - 357.4 (50.1)" "0.2 - 346.0 (46.4)"
[1] "hr=" "1.1"
D47V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 24(14Q32.2) MUTATED                   14             1
  DEL PEAK 24(14Q32.2) WILD-TYPE                 23             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 24(14Q32.2) MUTATED                                          25
  DEL PEAK 24(14Q32.2) WILD-TYPE                                        35
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 24(14Q32.2) MUTATED                    54
  DEL PEAK 24(14Q32.2) WILD-TYPE                 125
D47V4, multiclass
                                           clus
vv                                          DEL PEAK 24(14Q32.2) MUTATED
  DISTANT METASTASIS                                                  14
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           25
  REGIONAL LYMPH NODE                                                 54
                                           clus
vv                                          DEL PEAK 24(14Q32.2) WILD-TYPE
  DISTANT METASTASIS                                                    23
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             35
  REGIONAL LYMPH NODE                                                  125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 24(14Q32.2) MUTATED             5       1      11        4        6
  DEL PEAK 24(14Q32.2) WILD-TYPE           5       5      12        6       19
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 24(14Q32.2) MUTATED          8         0         3         3
  DEL PEAK 24(14Q32.2) WILD-TYPE        9        10        11         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 24(14Q32.2) MUTATED          13          3          9         16
  DEL PEAK 24(14Q32.2) WILD-TYPE        19         11         14         32
                                vv
clus                             STAGE IV
  DEL PEAK 24(14Q32.2) MUTATED          4
  DEL PEAK 24(14Q32.2) WILD-TYPE        8
D47V5, multiclass
             clus
vv            DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE
  I OR II NOS                            5                              5
  STAGE 0                                1                              5
  STAGE I                               11                             12
  STAGE IA                               4                              6
  STAGE IB                               6                             19
  STAGE II                               8                              9
  STAGE IIA                              0                             10
  STAGE IIB                              3                             11
  STAGE IIC                              3                              7
  STAGE III                             13                             19
  STAGE IIIA                             3                             11
  STAGE IIIB                             9                             14
  STAGE IIIC                            16                             32
  STAGE IV                               4                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 24(14Q32.2) MUTATED      22 22 15 19
  DEL PEAK 24(14Q32.2) WILD-TYPE    31 38 40 38
D47V6, multiclass
       clus
vv      DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE
  T0+T1                           22                             31
  T2                              22                             38
  T3                              15                             40
  T4                              19                             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 24(14Q32.2) MUTATED   47 22  7 13
  DEL PEAK 24(14Q32.2) WILD-TYPE 94 29 25 24
D47V7, multiclass
    clus
vv   DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE
  N0                           47                             94
  N1                           22                             29
  N2                            7                             25
  N3                           13                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 24(14Q32.2) MUTATED    87   0   1   0   3
  DEL PEAK 24(14Q32.2) WILD-TYPE 165   4   1   2   2
D47V8, multiclass
     clus
vv    DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE
  M0                            87                            165
  M1                             0                              4
  M1A                            1                              1
  M1B                            0                              2
  M1C                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                                cls
clus                              0  1
  DEL PEAK 24(14Q32.2) MUTATED   34 26
  DEL PEAK 24(14Q32.2) WILD-TYPE 70 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q32.2) MUTATED     34   26
  DEL PEAK 24(14Q32.2) WILD-TYPE   70   46
     clus
vv    DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE
  NO                            34                             70
  YES                           26                             46
[1] 2 2
[1] FALSE
D47V10, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q32.2) MUTATED    11  84
  DEL PEAK 24(14Q32.2) WILD-TYPE  23 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q32.2) MUTATED     11   84
  DEL PEAK 24(14Q32.2) WILD-TYPE   23  163
     clus
vv    DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE
  NO                            11                             23
  YES                           84                            163
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q32.2) MUTATED    37  58
  DEL PEAK 24(14Q32.2) WILD-TYPE  71 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q32.2) MUTATED     37   58
  DEL PEAK 24(14Q32.2) WILD-TYPE   71  115
        clus
vv       DEL PEAK 24(14Q32.2) MUTATED DEL PEAK 24(14Q32.2) WILD-TYPE
  FEMALE                           37                             71
  MALE                             58                            115
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(14Q32.2) MUTATED       2                         0    93
  DEL PEAK 24(14Q32.2) WILD-TYPE     3                         1   182
D47V13, multiclass
                           clus
vv                          DEL PEAK 24(14Q32.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               93
                           clus
vv                          DEL PEAK 24(14Q32.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q32.2) MUTATED     0  94
  DEL PEAK 24(14Q32.2) WILD-TYPE   3 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q32.2) MUTATED      0   94
  DEL PEAK 24(14Q32.2) WILD-TYPE    3  180
                        clus
vv                       DEL PEAK 24(14Q32.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       DEL PEAK 24(14Q32.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            180
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 25(15Q13.3) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(15Q13.3) MUTATED    28  38
  DEL PEAK 25(15Q13.3) WILD-TYPE 109  95
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                            66                            204 
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                            38                             95 
$`DEL PEAK 25(15Q13.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML 
       16.47        81.24        85.32        15.25        61.38         6.31 
TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A1HV 
       26.37        20.48        52.01        47.87        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-EB-A44R TCGA-EB-A5KH 
       35.80        51.12        39.19        25.15         0.20         0.13 
TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A20I TCGA-EE-A29L TCGA-EE-A29P 
        0.00         6.31         8.12         1.18         1.08        12.03 
TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC 
        8.09         9.67        47.21         5.42         8.84        47.51 
TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MT 
        9.53         7.96        14.56       111.78        56.02        23.05 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE 
        5.56       122.73         3.22        21.60        22.22         0.46 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19W TCGA-ER-A2NE TCGA-FS-A1YX 
       31.40        12.95         5.72        17.72         1.51         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM 
       23.80        15.52        19.53         7.17        12.89        47.38 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       14.20         5.98         2.27         0.20         0.13         0.16 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X 
       31.33        10.13        16.24        14.70        10.65        11.05 

$`DEL PEAK 25(15Q13.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       22.55        45.83        10.29         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        69.90        11.41        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98        46.32        82.29        13.32        24.00         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS 
       17.72         8.84        13.94        95.38         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       23.11         4.01         2.89         9.90        11.31        14.60 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       10.03        13.68         9.99        44.52        36.69         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       13.15         0.00        13.22         0.20        11.57        10.55 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.34         5.13         9.21         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         8.55         4.41        27.12         9.50 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.84         9.99         6.48         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22        23.90         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83        30.84         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       36.33        98.27         2.70         6.18        29.46        44.25 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       63.42       111.91        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       27.16       124.31        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD 
       15.95        12.72        22.92        21.60        16.14        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       13.94        33.60        18.61        38.40        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG 
       36.07        78.44        11.80         1.87        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       85.74         4.90         6.71         3.58         5.36        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       11.01        14.24         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        8.22        11.08        30.87        12.92        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
        5.23        53.85         3.22         7.36        28.73        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        6.41         0.99         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-QB-A6FS 
       24.85        84.72        15.42        12.16        11.84         5.79 

  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                         13.71                          14.09 
[1] "0.0 - 122.7 (13.7)" "0.0 - 124.3 (14.1)"
[1] "hr=" "1.4"
D48V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(15Q13.3) MUTATED    29  39
  DEL PEAK 25(15Q13.3) WILD-TYPE 113  95
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                            68                            208 
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                            39                             95 
$`DEL PEAK 25(15Q13.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML 
       16.57        95.74       103.10        58.06        86.93        13.87 
TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A1JX 
       39.75        51.68       135.75       137.92       151.53         6.41 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I8 
       66.25        48.89        36.03       117.21       194.83        53.92 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A20I 
       10.16        17.85        35.01         8.65        94.98        13.55 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GP 
        2.60        56.42        37.35        39.29       208.04        13.91 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       21.67        61.51        47.28        16.96       204.66       144.76 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 
      167.90        41.59        53.26       122.73       172.18        64.08 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19W 
       53.19        33.40        31.40        13.94         9.17       148.18 
TCGA-ER-A2NE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG 
       20.15        48.59       202.65        28.08        40.27         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       23.93       101.26       174.84        26.73        77.88         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D 
       47.54         0.16       117.93        10.13        64.44        39.58 
TCGA-GN-A4U9 TCGA-OD-A75X 
       12.62       294.77 

$`DEL PEAK 25(15Q13.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       31.59        90.90        43.43        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        69.90        11.87        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98        46.32       166.52        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS 
       18.38        10.03        15.06       110.93       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      125.19        54.67         3.65        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       25.18        22.95        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
      215.44        15.68        13.87        45.11         3.55        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
        6.35        12.20        29.82        27.22        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
      168.26        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       72.07        32.19        44.35        18.61        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      345.96        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
      101.95        14.30        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML 
       28.83        19.76       103.27       103.20        96.23       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
       47.54       248.65        43.23       103.56       136.47       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI 
      127.20        36.95        34.32        27.35       101.79       148.08 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       35.44        50.76        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 
       61.05        44.05       162.08        50.89        37.25        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
      210.08        15.16         7.00       216.92       228.59        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
        7.79        27.72        48.85       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       50.14        66.67        28.73        12.43        49.45        22.92 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
        2.40         9.90         7.23        14.04       120.46        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-QB-A6FS 
       62.79        32.48        46.36         6.67 

  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                          0.16                           2.40 
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                        294.77                         357.37 
  DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE 
                        48.065                         47.690 
[1] "0.2 - 294.8 (48.1)" "2.4 - 357.4 (47.7)"
[1] "hr=" "1.3"
D48V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 25(15Q13.3) MUTATED                    9             1
  DEL PEAK 25(15Q13.3) WILD-TYPE                 28             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 25(15Q13.3) MUTATED                                          16
  DEL PEAK 25(15Q13.3) WILD-TYPE                                        44
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 25(15Q13.3) MUTATED                    42
  DEL PEAK 25(15Q13.3) WILD-TYPE                 137
D48V4, multiclass
                                           clus
vv                                          DEL PEAK 25(15Q13.3) MUTATED
  DISTANT METASTASIS                                                   9
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           16
  REGIONAL LYMPH NODE                                                 42
                                           clus
vv                                          DEL PEAK 25(15Q13.3) WILD-TYPE
  DISTANT METASTASIS                                                    28
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             44
  REGIONAL LYMPH NODE                                                  137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 25(15Q13.3) MUTATED             0       2       9        2        5
  DEL PEAK 25(15Q13.3) WILD-TYPE          10       4      14        8       20
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 25(15Q13.3) MUTATED          3         1         4         4
  DEL PEAK 25(15Q13.3) WILD-TYPE       14         9        10         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 25(15Q13.3) MUTATED          10          4          6         10
  DEL PEAK 25(15Q13.3) WILD-TYPE        22         10         17         38
                                vv
clus                             STAGE IV
  DEL PEAK 25(15Q13.3) MUTATED          2
  DEL PEAK 25(15Q13.3) WILD-TYPE       10
D48V5, multiclass
             clus
vv            DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE
  I OR II NOS                            0                             10
  STAGE 0                                2                              4
  STAGE I                                9                             14
  STAGE IA                               2                              8
  STAGE IB                               5                             20
  STAGE II                               3                             14
  STAGE IIA                              1                              9
  STAGE IIB                              4                             10
  STAGE IIC                              4                              6
  STAGE III                             10                             22
  STAGE IIIA                             4                             10
  STAGE IIIB                             6                             17
  STAGE IIIC                            10                             38
  STAGE IV                               2                             10
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 25(15Q13.3) MUTATED      13 16  9 20
  DEL PEAK 25(15Q13.3) WILD-TYPE    40 44 46 37
D48V6, multiclass
       clus
vv      DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE
  T0+T1                           13                             40
  T2                              16                             44
  T3                               9                             46
  T4                              20                             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 25(15Q13.3) MUTATED    36   9   9   9
  DEL PEAK 25(15Q13.3) WILD-TYPE 105  42  23  28
D48V7, multiclass
    clus
vv   DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE
  N0                           36                            105
  N1                            9                             42
  N2                            9                             23
  N3                            9                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 25(15Q13.3) MUTATED    61   1   0   1   1
  DEL PEAK 25(15Q13.3) WILD-TYPE 191   3   2   1   4
D48V8, multiclass
     clus
vv    DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE
  M0                            61                            191
  M1                             1                              3
  M1A                            0                              2
  M1B                            1                              1
  M1C                            1                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                                cls
clus                              0  1
  DEL PEAK 25(15Q13.3) MUTATED   26 19
  DEL PEAK 25(15Q13.3) WILD-TYPE 78 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q13.3) MUTATED     26   19
  DEL PEAK 25(15Q13.3) WILD-TYPE   78   53
     clus
vv    DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE
  NO                            26                             78
  YES                           19                             53
[1] 2 2
[1] FALSE
D48V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q13.3) MUTATED     6  63
  DEL PEAK 25(15Q13.3) WILD-TYPE  28 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q13.3) MUTATED      6   63
  DEL PEAK 25(15Q13.3) WILD-TYPE   28  184
     clus
vv    DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE
  NO                             6                             28
  YES                           63                            184
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q13.3) MUTATED    26  43
  DEL PEAK 25(15Q13.3) WILD-TYPE  82 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q13.3) MUTATED     26   43
  DEL PEAK 25(15Q13.3) WILD-TYPE   82  130
        clus
vv       DEL PEAK 25(15Q13.3) MUTATED DEL PEAK 25(15Q13.3) WILD-TYPE
  FEMALE                           26                             82
  MALE                             43                            130
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(15Q13.3) MUTATED       2                         0    67
  DEL PEAK 25(15Q13.3) WILD-TYPE     3                         1   208
D48V13, multiclass
                           clus
vv                          DEL PEAK 25(15Q13.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               67
                           clus
vv                          DEL PEAK 25(15Q13.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q13.3) MUTATED     0  69
  DEL PEAK 25(15Q13.3) WILD-TYPE   3 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q13.3) MUTATED      0   69
  DEL PEAK 25(15Q13.3) WILD-TYPE    3  205
                        clus
vv                       DEL PEAK 25(15Q13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       DEL PEAK 25(15Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            205
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 26(15Q14) MUTATION ANALYSIS
D49V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(15Q14) MUTATED    28  40
  DEL PEAK 26(15Q14) WILD-TYPE 109  93
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                          68                          202 
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                          40                           93 
$`DEL PEAK 26(15Q14) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU 
       16.47        81.24        15.25        61.38         6.31        26.37 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A1HV 
       17.72        20.48        52.01        47.87        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44Q TCGA-EB-A44R 
       35.80        39.19        25.15         4.93        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A29L 
        0.13         0.00         6.31         8.12        12.20         1.08 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MC 
       12.03         8.09         9.67        47.21         8.84        47.51 
TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU 
        9.53         7.96        14.56       111.78        56.02         5.56 
TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A193 
      122.73         3.22        21.60        22.22         0.46        31.40 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19W 
       12.95        38.40         5.72         3.78         4.21        17.72 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE 
        6.58        22.49         3.45        23.80        15.52        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A4F8 TCGA-FS-A4FB 
        7.17        12.92        12.89        47.38        14.20         5.98 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D 
        2.27         0.13         0.16        10.13        16.24        14.70 
TCGA-GN-A4U9 TCGA-OD-A75X 
       10.65        11.05 

$`DEL PEAK 26(15Q14) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      114.67        46.98        46.32        82.29        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS 
       41.10         8.84        13.94        95.38         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       23.11         4.01         2.89         9.90        11.31        14.60 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
        0.00        13.22         0.20        11.57        10.55         1.12 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
        1.35         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R 
       38.63         8.55         4.41        27.12         9.50         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        23.90         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       36.33        98.27         2.70         6.18        29.46        44.25 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       63.42       111.91        25.08        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       27.16        23.05       124.31        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        15.95        12.72        22.92        21.60        16.14 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
       27.35        13.94        33.60        18.61        76.41        25.18 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        3.52        11.90        11.11       114.15        34.88        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 
       28.60        42.84        34.68         9.57        36.07        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        9.04         1.71        18.41        85.74         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        3.58         5.36        64.47        11.01        14.24         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.30         3.39        20.38         8.22        11.08        30.87 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       27.39         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY 
       28.73        10.78         6.41         0.20         0.99         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-QB-A6FS 
       15.42        12.16        11.84         5.79 

  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                           0                            0 
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                      122.73                       124.31 
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                      13.050                       14.715 
[1] "0.0 - 122.7 (13.1)" "0.0 - 124.3 (14.7)"
[1] "hr=" "1.5"
D49V2, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(15Q14) MUTATED    29  40
  DEL PEAK 26(15Q14) WILD-TYPE 113  94
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                          69                          207 
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                          40                           94 
$`DEL PEAK 26(15Q14) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU 
       16.57        95.74        58.06        86.93        13.87        39.75 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A6EC 
       18.38        51.68       135.75       137.92       151.53        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44Q 
       48.89        36.03       194.83        53.92        65.92        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 
       10.16        17.85        35.01         8.65        94.98        26.89 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 
        2.60        56.42        37.35        39.29       208.04        21.67 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
       61.51        47.28        16.96       204.66       144.76       167.90 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE 
       53.26       122.73       172.18        64.08        53.19        33.40 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19J 
       31.40        13.94        50.76         9.17        48.89         6.44 
TCGA-ER-A19W TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 
      148.18        80.32        46.98        48.59       202.65        28.08 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A4F8 
       40.27         9.70        47.38        23.93       101.26       174.84 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A266 TCGA-GN-A267 
       26.73        77.88        47.54         0.16        10.13        64.44 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X 
       39.58        12.62       294.77 

$`DEL PEAK 26(15Q14) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        46.98        46.32       166.52        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS 
      131.90        10.03        15.06       110.93       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.90        25.18        22.95       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       107.34        61.18        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       10.49       215.44        15.68        45.11         3.55        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
        6.35        12.20        29.82        27.22        33.73        14.70 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       72.07        32.19        44.35        18.61        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      345.96        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      101.95        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ 
      129.27        28.83        19.76       103.27       103.20        96.23 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      203.05        47.54       248.65        43.23       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       41.59       124.31        25.84         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD 
       23.47       138.81       127.20        36.95        34.32        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
      101.79       148.08        35.44        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       268.93       152.35       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
       44.05       162.08        50.89        37.25        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       33.21        92.98       174.21         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        7.00       216.92       228.59        20.91         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZP 
       48.85       357.37        53.52        15.45        32.75        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT 
       12.43        49.45         0.20        22.92         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        7.23        14.04       120.46       117.93        84.72        62.79 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-QB-A6FS 
       32.48        46.36         6.67 

  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                        0.16                         0.20 
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                      294.77                       357.37 
  DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE 
                       48.59                        47.54 
[1] "0.2 - 294.8 (48.6)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.3"
D49V3, continuous
                              vv
clus                           DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 26(15Q14) MUTATED                    9             1
  DEL PEAK 26(15Q14) WILD-TYPE                 28             3
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 26(15Q14) MUTATED                                          16
  DEL PEAK 26(15Q14) WILD-TYPE                                        44
                              vv
clus                           REGIONAL LYMPH NODE
  DEL PEAK 26(15Q14) MUTATED                    43
  DEL PEAK 26(15Q14) WILD-TYPE                 136
D49V4, multiclass
                                           clus
vv                                          DEL PEAK 26(15Q14) MUTATED
  DISTANT METASTASIS                                                 9
  PRIMARY TUMOR                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                         16
  REGIONAL LYMPH NODE                                               43
                                           clus
vv                                          DEL PEAK 26(15Q14) WILD-TYPE
  DISTANT METASTASIS                                                  28
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           44
  REGIONAL LYMPH NODE                                                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 26(15Q14) MUTATED             0       2      11        2        4
  DEL PEAK 26(15Q14) WILD-TYPE          10       4      12        8       21
                              vv
clus                           STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 26(15Q14) MUTATED          3         1         4         4        11
  DEL PEAK 26(15Q14) WILD-TYPE       14         9        10         6        21
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 26(15Q14) MUTATED            5          7          9        1
  DEL PEAK 26(15Q14) WILD-TYPE          9         16         39       11
D49V5, multiclass
             clus
vv            DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE
  I OR II NOS                          0                           10
  STAGE 0                              2                            4
  STAGE I                             11                           12
  STAGE IA                             2                            8
  STAGE IB                             4                           21
  STAGE II                             3                           14
  STAGE IIA                            1                            9
  STAGE IIB                            4                           10
  STAGE IIC                            4                            6
  STAGE III                           11                           21
  STAGE IIIA                           5                            9
  STAGE IIIB                           7                           16
  STAGE IIIC                           9                           39
  STAGE IV                             1                           11
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 26(15Q14) MUTATED      13 17  9 19
  DEL PEAK 26(15Q14) WILD-TYPE    40 43 46 38
D49V6, multiclass
       clus
vv      DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE
  T0+T1                         13                           40
  T2                            17                           43
  T3                             9                           46
  T4                            19                           38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  DEL PEAK 26(15Q14) MUTATED    35   9  10  10
  DEL PEAK 26(15Q14) WILD-TYPE 106  42  22  27
D49V7, multiclass
    clus
vv   DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE
  N0                         35                          106
  N1                          9                           42
  N2                         10                           22
  N3                         10                           27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B M1C
  DEL PEAK 26(15Q14) MUTATED    64   1   0   1   0
  DEL PEAK 26(15Q14) WILD-TYPE 188   3   2   1   5
D49V8, multiclass
     clus
vv    DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE
  M0                          64                          188
  M1                           1                            3
  M1A                          0                            2
  M1B                          1                            1
  M1C                          0                            5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                              cls
clus                            0  1
  DEL PEAK 26(15Q14) MUTATED   26 17
  DEL PEAK 26(15Q14) WILD-TYPE 78 55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(15Q14) MUTATED     26   17
  DEL PEAK 26(15Q14) WILD-TYPE   78   55
     clus
vv    DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE
  NO                          26                           78
  YES                         17                           55
[1] 2 2
[1] FALSE
D49V10, binary
                              cls
clus                             0   1
  DEL PEAK 26(15Q14) MUTATED     6  64
  DEL PEAK 26(15Q14) WILD-TYPE  28 183
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(15Q14) MUTATED      6   64
  DEL PEAK 26(15Q14) WILD-TYPE   28  183
     clus
vv    DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE
  NO                           6                           28
  YES                         64                          183
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, binary
                              cls
clus                             0   1
  DEL PEAK 26(15Q14) MUTATED    28  42
  DEL PEAK 26(15Q14) WILD-TYPE  80 131
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(15Q14) MUTATED     28   42
  DEL PEAK 26(15Q14) WILD-TYPE   80  131
        clus
vv       DEL PEAK 26(15Q14) MUTATED DEL PEAK 26(15Q14) WILD-TYPE
  FEMALE                         28                           80
  MALE                           42                          131
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(15Q14) MUTATED       3                         0    67
  DEL PEAK 26(15Q14) WILD-TYPE     2                         1   208
D49V13, multiclass
                           clus
vv                          DEL PEAK 26(15Q14) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             67
                           clus
vv                          DEL PEAK 26(15Q14) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                              cls
clus                             0   1
  DEL PEAK 26(15Q14) MUTATED     1  69
  DEL PEAK 26(15Q14) WILD-TYPE   2 205
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(15Q14) MUTATED      1   69
  DEL PEAK 26(15Q14) WILD-TYPE    2  205
                        clus
vv                       DEL PEAK 26(15Q14) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         69
                        clus
vv                       DEL PEAK 26(15Q14) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          205
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 27(15Q15.2) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q15.2) MUTATED    30  40
  DEL PEAK 27(15Q15.2) WILD-TYPE 107  93
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                            70                            200 
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                            40                             93 
$`DEL PEAK 27(15Q15.2) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU 
       16.47        81.24        15.25        61.38         6.31        26.37 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A1HV 
       17.72        20.48        52.01        47.87        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44Q TCGA-EB-A44R 
       35.80        39.19        25.15         4.93        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
        0.13         0.00         6.31         8.12         1.12        12.20 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 
        1.08        12.03         8.09         9.67        47.21         8.84 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
       47.51         9.53         7.96        14.56       111.78        56.02 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE 
        5.56       122.73         3.22        21.60        22.22         0.46 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19G 
       31.40        12.95        38.40         5.72         3.78       114.15 
TCGA-ER-A19J TCGA-ER-A19W TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 
        4.21        17.72         6.58        22.49         3.45        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZT 
       15.52        19.53         7.17        12.92        47.38        40.64 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A266 
       14.20         2.27         0.13         0.16        31.33        10.13 
TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X 
       16.24        14.70        10.65        11.05 

$`DEL PEAK 27(15Q15.2) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      114.67        46.98        46.32        82.29        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS 
       41.10         8.84        13.94        95.38         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       23.11         4.01         2.89         9.90        11.31        14.60 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
        0.00        13.22         0.20        11.57        10.55         1.35 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
        8.55         4.41        27.12         9.50         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        6.48         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ 
       98.27         2.70         6.18        29.46        44.25        63.42 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      111.91        25.08        26.99        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       23.05       124.31        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD 
       15.95        12.72        22.92        21.60        16.14        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       13.94        33.60        18.61        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.90        11.11        34.88        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       34.68         9.57        36.07        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL 
        1.51        13.08        12.62        11.74         9.04         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74         4.90         6.71         3.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       64.47        11.01        14.24         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP 
       20.38         8.22        11.08        30.87        12.89        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        49.15         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
        5.23        53.85         3.22         7.36        28.73        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT 
        5.98         6.41         0.20         0.99         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
        7.23        12.85        24.85        84.72        15.42        12.16 
TCGA-GN-A4U8 TCGA-QB-A6FS 
       11.84         5.79 

  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                             0                              0 
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                         13.71                          14.09 
[1] "0.0 - 122.7 (13.7)" "0.0 - 124.3 (14.1)"
[1] "hr=" "1.4"
D50V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q15.2) MUTATED    31  40
  DEL PEAK 27(15Q15.2) WILD-TYPE 111  94
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                            71                            205 
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                            40                             94 
$`DEL PEAK 27(15Q15.2) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU 
       16.57        95.74        58.06        86.93        13.87        39.75 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A6EC 
       18.38        51.68       135.75       137.92       151.53        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44Q 
       48.89        36.03       194.83        53.92        65.92        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       10.16        17.85        35.01         8.65        94.98        33.73 
TCGA-EE-A183 TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH 
       26.89         2.60        56.42        37.35        39.29       208.04 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       21.67        61.51        47.28        16.96       204.66       144.76 
TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
      167.90        53.26       122.73       172.18        64.08        53.19 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C 
       33.40        31.40        13.94        50.76         9.17        48.89 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19W TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FS-A1YX 
      268.93         6.44       148.18        80.32        46.98        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      202.65        28.08        40.27         9.70        47.38       101.26 
TCGA-FS-A1ZT TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 
       53.16       174.84        77.88        47.54         0.16       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X 
       10.13        64.44        39.58        12.62       294.77 

$`DEL PEAK 27(15Q15.2) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        46.98        46.32       166.52        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS 
      131.90        10.03        15.06       110.93       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.90        25.18        22.95       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       107.34        61.18        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       10.49       215.44        15.68        45.11         3.55        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 
        6.35        12.20        29.82        27.22        14.70        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       32.19        44.35        18.61        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       58.75        47.54        67.43       314.56       135.95        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       13.91        14.30        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML 
       28.83        19.76       103.27       103.20        96.23       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       103.56       136.47        41.59 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31        25.84         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH 
      138.81       127.20        36.95        34.32        27.35       101.79 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
      148.08        35.44        77.75        98.40        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       26.37       152.35       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       50.89        37.25        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
       16.37        31.27        32.05       247.04        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      174.21         4.90       210.08        15.16         7.00       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      228.59        20.91         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       53.52        15.45        32.75        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67        28.73        12.43        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       49.45         0.20        22.92         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
       14.04       120.46        84.72        62.79        32.48        46.36 
TCGA-QB-A6FS 
        6.67 

  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                          0.16                           0.20 
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                        294.77                         357.37 
  DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE 
                         48.89                          46.98 
[1] "0.2 - 294.8 (48.9)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.2"
D50V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 27(15Q15.2) MUTATED                    9             1
  DEL PEAK 27(15Q15.2) WILD-TYPE                 28             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 27(15Q15.2) MUTATED                                          16
  DEL PEAK 27(15Q15.2) WILD-TYPE                                        44
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 27(15Q15.2) MUTATED                    46
  DEL PEAK 27(15Q15.2) WILD-TYPE                 133
D50V4, multiclass
                                           clus
vv                                          DEL PEAK 27(15Q15.2) MUTATED
  DISTANT METASTASIS                                                   9
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           16
  REGIONAL LYMPH NODE                                                 46
                                           clus
vv                                          DEL PEAK 27(15Q15.2) WILD-TYPE
  DISTANT METASTASIS                                                    28
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             44
  REGIONAL LYMPH NODE                                                  133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 27(15Q15.2) MUTATED             1       2      11        2        4
  DEL PEAK 27(15Q15.2) WILD-TYPE           9       4      12        8       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 27(15Q15.2) MUTATED          3         1         4         4
  DEL PEAK 27(15Q15.2) WILD-TYPE       14         9        10         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 27(15Q15.2) MUTATED          11          5          7          9
  DEL PEAK 27(15Q15.2) WILD-TYPE        21          9         16         39
                                vv
clus                             STAGE IV
  DEL PEAK 27(15Q15.2) MUTATED          1
  DEL PEAK 27(15Q15.2) WILD-TYPE       11
D50V5, multiclass
             clus
vv            DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE
  I OR II NOS                            1                              9
  STAGE 0                                2                              4
  STAGE I                               11                             12
  STAGE IA                               2                              8
  STAGE IB                               4                             21
  STAGE II                               3                             14
  STAGE IIA                              1                              9
  STAGE IIB                              4                             10
  STAGE IIC                              4                              6
  STAGE III                             11                             21
  STAGE IIIA                             5                              9
  STAGE IIIB                             7                             16
  STAGE IIIC                             9                             39
  STAGE IV                               1                             11
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 27(15Q15.2) MUTATED      13 17 10 18
  DEL PEAK 27(15Q15.2) WILD-TYPE    40 43 45 39
D50V6, multiclass
       clus
vv      DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE
  T0+T1                           13                             40
  T2                              17                             43
  T3                              10                             45
  T4                              18                             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 27(15Q15.2) MUTATED    37   9  10  10
  DEL PEAK 27(15Q15.2) WILD-TYPE 104  42  22  27
D50V7, multiclass
    clus
vv   DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE
  N0                           37                            104
  N1                            9                             42
  N2                           10                             22
  N3                           10                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 27(15Q15.2) MUTATED    66   1   0   1   0
  DEL PEAK 27(15Q15.2) WILD-TYPE 186   3   2   1   5
D50V8, multiclass
     clus
vv    DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE
  M0                            66                            186
  M1                             1                              3
  M1A                            0                              2
  M1B                            1                              1
  M1C                            0                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                                cls
clus                              0  1
  DEL PEAK 27(15Q15.2) MUTATED   28 17
  DEL PEAK 27(15Q15.2) WILD-TYPE 76 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q15.2) MUTATED     28   17
  DEL PEAK 27(15Q15.2) WILD-TYPE   76   55
     clus
vv    DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE
  NO                            28                             76
  YES                           17                             55
[1] 2 2
[1] FALSE
D50V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q15.2) MUTATED     6  67
  DEL PEAK 27(15Q15.2) WILD-TYPE  28 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q15.2) MUTATED      6   67
  DEL PEAK 27(15Q15.2) WILD-TYPE   28  180
     clus
vv    DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE
  NO                             6                             28
  YES                           67                            180
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q15.2) MUTATED    30  43
  DEL PEAK 27(15Q15.2) WILD-TYPE  78 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q15.2) MUTATED     30   43
  DEL PEAK 27(15Q15.2) WILD-TYPE   78  130
        clus
vv       DEL PEAK 27(15Q15.2) MUTATED DEL PEAK 27(15Q15.2) WILD-TYPE
  FEMALE                           30                             78
  MALE                             43                            130
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(15Q15.2) MUTATED       3                         0    70
  DEL PEAK 27(15Q15.2) WILD-TYPE     2                         1   205
D50V13, multiclass
                           clus
vv                          DEL PEAK 27(15Q15.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               70
                           clus
vv                          DEL PEAK 27(15Q15.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q15.2) MUTATED     1  72
  DEL PEAK 27(15Q15.2) WILD-TYPE   2 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q15.2) MUTATED      1   72
  DEL PEAK 27(15Q15.2) WILD-TYPE    2  202
                        clus
vv                       DEL PEAK 27(15Q15.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           72
                        clus
vv                       DEL PEAK 27(15Q15.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            202
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 28(16P13.3) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(16P13.3) MUTATED    26  25
  DEL PEAK 28(16P13.3) WILD-TYPE 111 108
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            51                            219 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            25                            108 
$`DEL PEAK 28(16P13.3) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JL 
      111.09        32.42        22.55        45.83        68.22        92.42 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51K TCGA-D3-A51N TCGA-D9-A6EC 
       64.44       114.67        61.38        17.72         8.84        13.22 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20I 
       35.80        13.68         0.20         8.12         1.12         1.18 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       11.15         1.08        27.12         8.68         8.09        11.31 
TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MK 
       34.29        30.84        36.33         8.84        98.27       111.78 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JA 
       56.02        21.60         5.56       122.73        21.60        22.22 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19E TCGA-FS-A1Z0 TCGA-FS-A1ZD 
       33.60        31.40        12.95        11.90        23.80         8.22 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 
       40.64         8.68        27.39         0.99         0.13        24.85 
TCGA-GN-A267 TCGA-GN-A26D TCGA-OD-A75X 
       16.24        14.70        11.05 

$`DEL PEAK 28(16P13.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       16.47         8.52        70.16       110.79        28.08        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       10.29        85.32         8.38        21.14        88.50        69.90 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       11.41        30.87         7.50        36.16         6.31        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       45.11        15.25        46.98        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T 
       80.22        42.71        15.09        41.10        20.48        13.94 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       95.38        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01         2.89         9.90        11.31        14.60        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        39.19         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.13         0.00         0.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
       13.22         0.20        11.57        10.55         6.31         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        9.21         7.99         9.90        37.97        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        4.41         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        6.48         2.43        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.39        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       13.02        34.98         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56        63.42       111.91 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       25.08        26.99        29.65        27.16        23.05       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
        3.22        22.92        21.60        16.14        27.35         0.46 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       13.94        18.61        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.78         3.52        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74         4.90         6.71         3.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30         3.39        20.38        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
        8.81        49.15         0.82         5.23        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.20         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
       12.85        31.33        84.72        10.13        15.42        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       11.84        10.65         5.79 

  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                         21.60                          13.32 
[1] "0.1 - 122.7 (21.6)" "0.0 - 124.3 (13.3)"
[1] "hr=" "1.2"
D51V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(16P13.3) MUTATED    27  25
  DEL PEAK 28(16P13.3) WILD-TYPE 115 109
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            52                            224 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            25                            109 
$`DEL PEAK 28(16P13.3) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JL 
      112.04       112.57        31.59        90.90       168.00       171.58 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51K TCGA-D3-A51N TCGA-D9-A6EC 
       66.08       130.72        86.93        18.38        10.03        66.25 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A181 
       36.03       176.55        10.16         3.55        94.98        33.73 
TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A29X 
       13.55        13.97         2.60        44.35       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       46.82        67.43       101.95        94.82        21.67       129.27 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J5 
      144.76       167.90        43.23        53.26       122.73        36.95 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19E TCGA-FS-A1Z0 
       53.19       148.08        31.40        13.94        13.02       202.65 
TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU 
       53.52        53.16        26.56        49.48        22.92        47.54 
TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A26D TCGA-OD-A75X 
      120.46        64.44        39.58       294.77 

$`DEL PEAK 28(16P13.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       16.57        16.67        71.80       133.25        28.08        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       115.53        69.90 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       11.87        48.76       113.52        42.08        12.10        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       45.11        58.06        46.98        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T 
      161.85        43.69        40.14       131.90        51.68        15.06 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      110.93       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        22.95        48.89       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      194.83        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        17.85        45.11        35.01        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       12.20        29.82        27.22         8.65        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       109.64       151.27        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        39.62        72.07        32.19 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        37.35        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       25.87       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48        90.97        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       44.88        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      103.20        16.96       204.66        96.23       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      248.65       103.56       136.47        41.59       124.31        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        64.08        34.32        27.35        33.40       101.79 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      174.21         4.90       210.08        15.16         7.00       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
      148.80        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.20         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
      117.93        84.72        10.13        62.79        32.48        46.36 
TCGA-GN-A4U9 TCGA-QB-A6FS 
       12.62         6.67 

  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                          2.60                           0.16 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        294.77                         357.37 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        53.225                         47.330 
[1] "2.6 - 294.8 (53.2)" "0.2 - 357.4 (47.3)"
[1] "hr=" "1.1"
D51V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 28(16P13.3) MUTATED                    7             1
  DEL PEAK 28(16P13.3) WILD-TYPE                 30             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 28(16P13.3) MUTATED                                           7
  DEL PEAK 28(16P13.3) WILD-TYPE                                        53
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 28(16P13.3) MUTATED                    37
  DEL PEAK 28(16P13.3) WILD-TYPE                 142
D51V4, multiclass
                                           clus
vv                                          DEL PEAK 28(16P13.3) MUTATED
  DISTANT METASTASIS                                                   7
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            7
  REGIONAL LYMPH NODE                                                 37
                                           clus
vv                                          DEL PEAK 28(16P13.3) WILD-TYPE
  DISTANT METASTASIS                                                    30
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             53
  REGIONAL LYMPH NODE                                                  142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 28(16P13.3) MUTATED             3       2       4        3        5
  DEL PEAK 28(16P13.3) WILD-TYPE           7       4      19        7       20
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 28(16P13.3) MUTATED          2         2         3         3
  DEL PEAK 28(16P13.3) WILD-TYPE       15         8        11         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 28(16P13.3) MUTATED           7          3          6          5
  DEL PEAK 28(16P13.3) WILD-TYPE        25         11         17         43
                                vv
clus                             STAGE IV
  DEL PEAK 28(16P13.3) MUTATED          2
  DEL PEAK 28(16P13.3) WILD-TYPE       10
D51V5, multiclass
             clus
vv            DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  I OR II NOS                            3                              7
  STAGE 0                                2                              4
  STAGE I                                4                             19
  STAGE IA                               3                              7
  STAGE IB                               5                             20
  STAGE II                               2                             15
  STAGE IIA                              2                              8
  STAGE IIB                              3                             11
  STAGE IIC                              3                              7
  STAGE III                              7                             25
  STAGE IIIA                             3                             11
  STAGE IIIB                             6                             17
  STAGE IIIC                             5                             43
  STAGE IV                               2                             10
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 28(16P13.3) MUTATED       7 13  8 12
  DEL PEAK 28(16P13.3) WILD-TYPE    46 47 47 45
D51V6, multiclass
       clus
vv      DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  T0+T1                            7                             46
  T2                              13                             47
  T3                               8                             47
  T4                              12                             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 28(16P13.3) MUTATED    30  10   7   3
  DEL PEAK 28(16P13.3) WILD-TYPE 111  41  25  34
D51V7, multiclass
    clus
vv   DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  N0                           30                            111
  N1                           10                             41
  N2                            7                             25
  N3                            3                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 28(16P13.3) MUTATED    48   0   0   0   2
  DEL PEAK 28(16P13.3) WILD-TYPE 204   4   2   2   3
D51V8, multiclass
     clus
vv    DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  M0                            48                            204
  M1                             0                              4
  M1A                            0                              2
  M1B                            0                              2
  M1C                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
                                cls
clus                              0  1
  DEL PEAK 28(16P13.3) MUTATED   22 14
  DEL PEAK 28(16P13.3) WILD-TYPE 82 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED     22   14
  DEL PEAK 28(16P13.3) WILD-TYPE   82   58
     clus
vv    DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  NO                            22                             82
  YES                           14                             58
[1] 2 2
[1] FALSE
D51V10, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED     2  51
  DEL PEAK 28(16P13.3) WILD-TYPE  32 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED      2   51
  DEL PEAK 28(16P13.3) WILD-TYPE   32  196
     clus
vv    DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  NO                             2                             32
  YES                           51                            196
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED    25  28
  DEL PEAK 28(16P13.3) WILD-TYPE  83 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED     25   28
  DEL PEAK 28(16P13.3) WILD-TYPE   83  145
        clus
vv       DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  FEMALE                           25                             83
  MALE                             28                            145
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(16P13.3) MUTATED       1                         1    51
  DEL PEAK 28(16P13.3) WILD-TYPE     4                         0   224
D51V13, multiclass
                           clus
vv                          DEL PEAK 28(16P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               51
                           clus
vv                          DEL PEAK 28(16P13.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED     2  51
  DEL PEAK 28(16P13.3) WILD-TYPE   1 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED      2   51
  DEL PEAK 28(16P13.3) WILD-TYPE    1  223
                        clus
vv                       DEL PEAK 28(16P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           51
                        clus
vv                       DEL PEAK 28(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            223
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 29(16Q12.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 29(16Q12.1) MUTATED   42 46
  DEL PEAK 29(16Q12.1) WILD-TYPE 95 87
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            88                            182 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            46                             87 
$`DEL PEAK 29(16Q12.1) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB 
      111.09        32.42       110.79        45.83        10.29        68.22 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       69.90        30.87        92.42        56.19        64.44       114.67 
TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A5GS TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HW 
       61.38         8.84         6.97         2.89        13.22        35.80 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG 
       13.68         9.99        17.56        14.83         0.20         0.00 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I 
        6.31         8.12         1.12         4.31         4.34         1.18 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        9.90        37.97        11.15         1.08        27.12         9.50 
TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC 
       12.03         8.68         8.09        11.31         9.67        34.29 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MJ 
       47.21        30.84         5.42         8.84         9.53        63.42 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU 
      111.78        56.02        25.08        21.60        27.16         5.56 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA 
      122.73        30.15        13.81        22.92        21.60        22.22 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19N 
       33.60        31.40        12.95        25.18        11.90        42.84 
TCGA-ER-A19W TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZP 
       17.72        23.80         7.30         3.39        11.08        52.08 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FW-A3I3 
       40.64         8.68        27.39         3.22         7.36         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.99         0.13         7.23        12.85        24.85        31.33 
TCGA-GN-A267 TCGA-GN-A26D TCGA-OD-A75X TCGA-QB-A6FS 
       16.24        14.70        11.05         5.79 

$`DEL PEAK 29(16Q12.1) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
       16.47         8.52        70.16        28.08        22.55        81.24 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG 
       85.32         8.38        21.14        88.50        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       36.16         6.31        45.11        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
        1.55        23.11         4.01         9.90        11.31        14.60 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       48.79        51.12        10.03        39.19        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       13.15         0.13         0.00        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F 
       10.55         1.35        12.20         5.13        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q 
        9.21         7.99        38.63         8.55         4.41         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84         9.99         6.48         2.43        49.22        23.90 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
        8.94        39.39        17.98        34.92        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        28.31        33.83         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       34.98        36.33        98.27         2.70         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP 
       29.46        44.25         7.96        14.56       111.91        26.99 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG 
       29.65        23.05       124.31        25.84         3.68        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       12.72         3.22        21.60        16.14        27.35         0.46 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       13.94        18.61        38.40         5.72        76.41         3.78 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
       28.60        34.68         9.57        36.07        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        6.71         3.58         5.36        64.47         3.45        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       14.24        15.52         7.33        20.38         8.22        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        7.17        30.87        12.92        12.89        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 
        8.81        49.15         0.82         5.23        53.85        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV 
       14.20        10.78         5.98         6.41         2.27         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
        0.43         9.90        84.72        10.13        15.42        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 
       11.84        10.65 

  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                             0                              0 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                        14.255                         14.070 
[1] "0.0 - 122.7 (14.3)" "0.0 - 124.3 (14.1)"
[1] "hr=" "1.1"
D52V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 29(16Q12.1) MUTATED   45 46
  DEL PEAK 29(16Q12.1) WILD-TYPE 97 88
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            91                            185 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            46                             88 
$`DEL PEAK 29(16Q12.1) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB 
      112.04       112.57       133.25        90.90        43.43       168.00 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       69.90        48.76       171.58        56.19        66.08       130.72 
TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
       86.93        10.03         7.43       151.53        54.67         3.25 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-DA-A3F8 
       66.25        36.03       176.55        35.93       215.44        15.68 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       10.16        45.11         3.55         8.65        94.98        33.73 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        4.96       151.27        13.55        80.61        47.84        13.97 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X 
        2.60        44.35        18.61        56.42       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP 
       46.82        39.29        67.43       208.04       101.95        13.91 
TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
       21.67        47.28        96.23       144.76       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
       43.23       136.47        53.26       122.73        54.51        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
      127.20        36.95        53.19       148.08        31.40        13.94 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19N TCGA-ER-A19W TCGA-FS-A1Z0 TCGA-FS-A1ZA 
       98.40        13.02        44.05       148.18       202.65        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       48.85        15.45        74.73        53.16        26.56        49.48 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO 
       50.14        66.67         0.20        22.92        47.54         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D TCGA-OD-A75X 
       14.04       120.46       117.93        64.44        39.58       294.77 
TCGA-QB-A6FS 
        6.67 

$`DEL PEAK 29(16Q12.1) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
       16.57        16.67        71.80        28.08        31.59        95.74 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG 
      103.10        65.49        23.77       115.53        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       42.08        12.10        45.11        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 
      166.19       125.19         3.65         6.41        11.34         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        22.95        48.89       117.21        20.38       194.83 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN 
       28.60        10.49        13.87        17.85        35.01        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
        6.35        12.20        29.82        27.22        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E 
       68.15       109.64        78.87       168.26        63.35        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       72.07        32.19        37.35        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       25.87       102.90        24.43        58.75        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      135.95        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       90.97        14.30        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       28.83        19.76        61.51       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
      204.66       203.05       248.65       103.56        41.59       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       25.84         3.68        23.47       138.81       172.18        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 
       34.32        27.35        33.40       101.79        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        48.89        12.59        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21         4.90       210.08        15.16         7.00 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        40.27         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY 
       23.93       101.26       133.55        11.41       148.80        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 
       49.45        77.88         0.16         2.40         9.90        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        62.79        32.48        46.36        12.62 

  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                          0.20                           0.16 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                        294.77                         357.37 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                         49.48                          46.98 
[1] "0.2 - 294.8 (49.5)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.1"
D52V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 29(16Q12.1) MUTATED                   14             1
  DEL PEAK 29(16Q12.1) WILD-TYPE                 23             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 29(16Q12.1) MUTATED                                          16
  DEL PEAK 29(16Q12.1) WILD-TYPE                                        44
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 29(16Q12.1) MUTATED                    60
  DEL PEAK 29(16Q12.1) WILD-TYPE                 119
D52V4, multiclass
                                           clus
vv                                          DEL PEAK 29(16Q12.1) MUTATED
  DISTANT METASTASIS                                                  14
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           16
  REGIONAL LYMPH NODE                                                 60
                                           clus
vv                                          DEL PEAK 29(16Q12.1) WILD-TYPE
  DISTANT METASTASIS                                                    23
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             44
  REGIONAL LYMPH NODE                                                  119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 29(16Q12.1) MUTATED             4       3       5        4        8
  DEL PEAK 29(16Q12.1) WILD-TYPE           6       3      18        6       17
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 29(16Q12.1) MUTATED          7         2         7         6
  DEL PEAK 29(16Q12.1) WILD-TYPE       10         8         7         4
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 29(16Q12.1) MUTATED          10          3          8         10
  DEL PEAK 29(16Q12.1) WILD-TYPE        22         11         15         38
                                vv
clus                             STAGE IV
  DEL PEAK 29(16Q12.1) MUTATED          4
  DEL PEAK 29(16Q12.1) WILD-TYPE        8
D52V5, multiclass
             clus
vv            DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  I OR II NOS                            4                              6
  STAGE 0                                3                              3
  STAGE I                                5                             18
  STAGE IA                               4                              6
  STAGE IB                               8                             17
  STAGE II                               7                             10
  STAGE IIA                              2                              8
  STAGE IIB                              7                              7
  STAGE IIC                              6                              4
  STAGE III                             10                             22
  STAGE IIIA                             3                             11
  STAGE IIIB                             8                             15
  STAGE IIIC                            10                             38
  STAGE IV                               4                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 29(16Q12.1) MUTATED      14 18 18 20
  DEL PEAK 29(16Q12.1) WILD-TYPE    39 42 37 37
D52V6, multiclass
       clus
vv      DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  T0+T1                           14                             39
  T2                              18                             42
  T3                              18                             37
  T4                              20                             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 29(16Q12.1) MUTATED   51 15  9  8
  DEL PEAK 29(16Q12.1) WILD-TYPE 90 36 23 29
D52V7, multiclass
    clus
vv   DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  N0                           51                             90
  N1                           15                             36
  N2                            9                             23
  N3                            8                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 29(16Q12.1) MUTATED    79   1   0   1   3
  DEL PEAK 29(16Q12.1) WILD-TYPE 173   3   2   1   2
D52V8, multiclass
     clus
vv    DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  M0                            79                            173
  M1                             1                              3
  M1A                            0                              2
  M1B                            1                              1
  M1C                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                                cls
clus                              0  1
  DEL PEAK 29(16Q12.1) MUTATED   38 25
  DEL PEAK 29(16Q12.1) WILD-TYPE 66 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED     38   25
  DEL PEAK 29(16Q12.1) WILD-TYPE   66   47
     clus
vv    DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  NO                            38                             66
  YES                           25                             47
[1] 2 2
[1] FALSE
D52V10, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED     9  83
  DEL PEAK 29(16Q12.1) WILD-TYPE  25 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED      9   83
  DEL PEAK 29(16Q12.1) WILD-TYPE   25  164
     clus
vv    DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  NO                             9                             25
  YES                           83                            164
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED    41  51
  DEL PEAK 29(16Q12.1) WILD-TYPE  67 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED     41   51
  DEL PEAK 29(16Q12.1) WILD-TYPE   67  122
        clus
vv       DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  FEMALE                           41                             67
  MALE                             51                            122
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16Q12.1) MUTATED       1                         1    90
  DEL PEAK 29(16Q12.1) WILD-TYPE     4                         0   185
D52V13, multiclass
                           clus
vv                          DEL PEAK 29(16Q12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               90
                           clus
vv                          DEL PEAK 29(16Q12.1) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED     1  90
  DEL PEAK 29(16Q12.1) WILD-TYPE   2 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED      1   90
  DEL PEAK 29(16Q12.1) WILD-TYPE    2  184
                        clus
vv                       DEL PEAK 29(16Q12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       DEL PEAK 29(16Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            184
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 30(16Q24.3) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(16Q24.3) MUTATED   45 51
  DEL PEAK 30(16Q24.3) WILD-TYPE 92 82
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                            96                            174 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                            51                             82 
$`DEL PEAK 30(16Q24.3) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
      111.09        32.42       110.79        22.55        45.83        10.29 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN 
       88.50        68.22        69.90        30.87        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51N 
       64.44       114.67        61.38        13.32        26.37         8.84 
TCGA-D3-A5GO TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 
       47.87         2.89        11.31        13.22        35.80        13.68 
TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EE-A17Z TCGA-EE-A180 
        9.99        14.83         0.20         0.00         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B 
        1.12        12.20         4.31         4.34         1.18         9.90 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X 
       11.15         4.41        27.12        12.03         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP 
       11.31         9.67        34.29        47.21        30.84         5.42 
TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        8.84         9.53        44.25        14.56        63.42       111.78 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
       56.02        21.60         5.56       122.73        30.15        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.92        21.60        22.22        13.94        33.60        31.40 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
       12.95        25.18        11.11        42.84         9.57        17.72 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZF 
        1.87         1.71         3.58        23.80         3.39        11.08 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       12.92        52.08        40.64         8.68        27.39         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
        3.22         7.36         0.99         0.13         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-OD-A75X TCGA-QB-A6FS 
       24.85        16.24        15.42        14.70        11.05         5.79 

$`DEL PEAK 30(16Q24.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 
       16.47         8.52        70.16        28.08        81.24        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
        8.38        21.14        11.41         7.50        36.16         6.31 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
       45.11        15.25        46.98        46.32        82.29        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       15.09        41.10        17.72        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 
       52.01         1.55         6.97        23.11         4.01         9.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 
       14.60        48.79        51.12        10.03        39.19        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN 
        7.00        17.56        13.15         0.13         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20B 
        0.20        11.57        10.55         1.35         5.13        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        5.13         9.21         7.99        37.97        38.63         8.55 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        1.08         9.50         8.09         8.84         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
        2.43        49.22        23.90         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       33.83         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2ML 
        2.70         6.18        47.51        29.46         7.96       111.91 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       25.08        26.99        29.65        27.16        23.05       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       25.84         3.68        15.95        12.72         3.22        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       16.14        27.35         0.46        18.61        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       76.41         3.78         3.52        11.90       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 
        4.21        13.45        28.60        34.68        36.07        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       11.80         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        6.58        22.49        18.41        85.74         4.90         6.71 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.36        64.47         3.45        11.01        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.33         7.30        20.38         8.22        19.53         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        12.89        47.38         8.65         8.81        49.15 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23        53.85        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         2.27         0.20         0.16         0.43         9.90 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       31.33        84.72        10.13        12.16        11.84        10.65 

  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                        13.745                         14.420 
[1] "0.0 - 122.7 (13.7)" "0.0 - 124.3 (14.4)"
[1] "hr=" "1.1"
D53V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(16Q24.3) MUTATED   48 51
  DEL PEAK 30(16Q24.3) WILD-TYPE 94 83
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                            99                            177 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                            51                             83 
$`DEL PEAK 30(16Q24.3) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
      112.04       112.57       133.25        31.59        90.90        43.43 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN 
      115.53       168.00        69.90        48.76       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51N 
       66.08       130.72        86.93        60.23        39.75        10.03 
TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6EA 
      137.92       151.53        54.67         3.65         3.25        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EB-A44R 
       66.25        36.03       176.55        35.93        15.68        10.16 
TCGA-EB-A5SG TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       45.11         8.65        94.98        33.73        26.89         4.96 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M 
      151.27        13.55        80.61        13.97        32.19        44.35 
TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC 
       56.42       171.55        17.92        46.82        39.29        67.43 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MG 
      208.04       101.95        13.91        21.67        47.28       103.20 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU 
      204.66        96.23       144.76       167.90        43.23        53.26 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA 
      122.73        54.51        13.81       127.20        36.95        53.19 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19F 
      101.79       148.08        31.40        13.94        98.40        26.37 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A7U8 
       44.05        50.89       148.18        23.34        33.21        15.16 
TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZT 
      202.65        48.85        15.45        47.38        74.73        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FW-A3R5 
       26.56        49.48        27.09        50.14        66.67        22.92 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 
       47.54         7.23        14.04       120.46        64.44        62.79 
TCGA-GN-A26D TCGA-OD-A75X TCGA-QB-A6FS 
       39.58       294.77         6.67 

$`DEL PEAK 30(16Q24.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 
       16.57        16.67        71.80        28.08        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       65.49        23.77        11.87       113.52        42.08        12.10 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
       45.11        58.06        46.98        46.32       166.52        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       40.14       131.90        18.38        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1JX TCGA-D9-A3Z1 
      135.75       166.19         7.43       125.19         6.41        11.34 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        22.95        48.89       117.21        20.38       194.83 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH 
       28.60        10.49       215.44        13.87        17.85        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.55        52.01         6.35        12.20        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.70        68.15       109.64        78.87       168.26        63.35 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q 
       47.84        39.62        72.07         2.60        18.61        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        55.92       345.96        25.87       102.90        24.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       58.75        47.54       314.56       135.95        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        75.48        90.97        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
      103.27        16.96       203.05        47.54       248.65       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG 
      136.47        41.59       124.31        25.84         3.68        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
      138.81       172.18        64.08        34.32        27.35        33.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       35.44        50.76         9.17        77.75        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
      162.08        37.25        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       31.27        32.05       247.04        80.32        46.98        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
      174.21         4.90       210.08         7.00       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      228.59        20.91        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
       53.52        40.27         9.70        32.75        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 
      133.55        11.41       148.80        27.02        77.82        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.16         2.40         9.90       117.93        84.72        10.13 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48        46.36        12.62 

  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                          3.25                           0.16 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                        294.77                         357.37 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                         50.14                          46.98 
[1] "3.2 - 294.8 (50.1)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.1"
D53V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 30(16Q24.3) MUTATED                   16             2
  DEL PEAK 30(16Q24.3) WILD-TYPE                 21             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 30(16Q24.3) MUTATED                                          18
  DEL PEAK 30(16Q24.3) WILD-TYPE                                        42
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 30(16Q24.3) MUTATED                    64
  DEL PEAK 30(16Q24.3) WILD-TYPE                 115
D53V4, multiclass
                                           clus
vv                                          DEL PEAK 30(16Q24.3) MUTATED
  DISTANT METASTASIS                                                  16
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           18
  REGIONAL LYMPH NODE                                                 64
                                           clus
vv                                          DEL PEAK 30(16Q24.3) WILD-TYPE
  DISTANT METASTASIS                                                    21
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             42
  REGIONAL LYMPH NODE                                                  115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 30(16Q24.3) MUTATED             3       4       6        5        7
  DEL PEAK 30(16Q24.3) WILD-TYPE           7       2      17        5       18
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 30(16Q24.3) MUTATED          7         2        10         6
  DEL PEAK 30(16Q24.3) WILD-TYPE       10         8         4         4
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 30(16Q24.3) MUTATED          10          5          9         11
  DEL PEAK 30(16Q24.3) WILD-TYPE        22          9         14         37
                                vv
clus                             STAGE IV
  DEL PEAK 30(16Q24.3) MUTATED          3
  DEL PEAK 30(16Q24.3) WILD-TYPE        9
D53V5, multiclass
             clus
vv            DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  I OR II NOS                            3                              7
  STAGE 0                                4                              2
  STAGE I                                6                             17
  STAGE IA                               5                              5
  STAGE IB                               7                             18
  STAGE II                               7                             10
  STAGE IIA                              2                              8
  STAGE IIB                             10                              4
  STAGE IIC                              6                              4
  STAGE III                             10                             22
  STAGE IIIA                             5                              9
  STAGE IIIB                             9                             14
  STAGE IIIC                            11                             37
  STAGE IV                               3                              9
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 30(16Q24.3) MUTATED      16 19 21 22
  DEL PEAK 30(16Q24.3) WILD-TYPE    37 41 34 35
D53V6, multiclass
       clus
vv      DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  T0+T1                           16                             37
  T2                              19                             41
  T3                              21                             34
  T4                              22                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 30(16Q24.3) MUTATED   57 16 11  9
  DEL PEAK 30(16Q24.3) WILD-TYPE 84 35 21 28
D53V7, multiclass
    clus
vv   DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  N0                           57                             84
  N1                           16                             35
  N2                           11                             21
  N3                            9                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 30(16Q24.3) MUTATED    90   0   1   1   2
  DEL PEAK 30(16Q24.3) WILD-TYPE 162   4   1   1   3
D53V8, multiclass
     clus
vv    DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  M0                            90                            162
  M1                             0                              4
  M1A                            1                              1
  M1B                            1                              1
  M1C                            2                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                                cls
clus                              0  1
  DEL PEAK 30(16Q24.3) MUTATED   41 26
  DEL PEAK 30(16Q24.3) WILD-TYPE 63 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.3) MUTATED     41   26
  DEL PEAK 30(16Q24.3) WILD-TYPE   63   46
     clus
vv    DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  NO                            41                             63
  YES                           26                             46
[1] 2 2
[1] FALSE
D53V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q24.3) MUTATED    10  91
  DEL PEAK 30(16Q24.3) WILD-TYPE  24 156
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.3) MUTATED     10   91
  DEL PEAK 30(16Q24.3) WILD-TYPE   24  156
     clus
vv    DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  NO                            10                             24
  YES                           91                            156
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q24.3) MUTATED    44  57
  DEL PEAK 30(16Q24.3) WILD-TYPE  64 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.3) MUTATED     44   57
  DEL PEAK 30(16Q24.3) WILD-TYPE   64  116
        clus
vv       DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  FEMALE                           44                             64
  MALE                             57                            116
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(16Q24.3) MUTATED       1                         1    99
  DEL PEAK 30(16Q24.3) WILD-TYPE     4                         0   176
D53V13, multiclass
                           clus
vv                          DEL PEAK 30(16Q24.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               99
                           clus
vv                          DEL PEAK 30(16Q24.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q24.3) MUTATED     1  99
  DEL PEAK 30(16Q24.3) WILD-TYPE   2 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.3) MUTATED      1   99
  DEL PEAK 30(16Q24.3) WILD-TYPE    2  175
                        clus
vv                       DEL PEAK 30(16Q24.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       DEL PEAK 30(16Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            175
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 31(19P13.3) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(19P13.3) MUTATED    36  42
  DEL PEAK 31(19P13.3) WILD-TYPE 101  91
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            78                            192 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            42                             91 
$`DEL PEAK 31(19P13.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JL 
       16.47        22.55        81.24        10.29        11.41        92.42 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV 
       13.94        95.38        52.01         2.89        11.31        48.79 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       35.80        10.03        44.52        36.69        25.15         4.93 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A185 
        6.64        17.56         0.20         0.00        11.57         4.31 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        9.21         1.18        37.97        11.15         8.55         4.41 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB 
        9.50         2.43         8.09        11.31         8.94        39.39 
TCGA-EE-A2GM TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MQ 
       28.31        13.02        36.33        44.25        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J4 
       27.16        23.05       122.73        25.84         3.68        22.92 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19C 
       21.60        22.22        27.35        31.40        25.18         3.78 
TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG 
       34.88        28.60         9.57        17.72         1.87        12.62 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZD 
       11.74        22.49        18.41        85.74         4.90         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FB 
       11.08        30.87         8.65        40.64        27.39         5.98 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 
        2.27         0.13         0.16         7.23        24.85        15.42 

$`DEL PEAK 31(19P13.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       45.83        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       69.90        30.87         7.50        36.16         6.31        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR 
       41.10        17.72         8.84        20.48        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        6.97        23.11         4.01         9.90        13.22        14.60 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 
       51.12        39.19        13.68         9.99        22.36        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN 
        7.00        14.83        13.15         0.13         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        0.20        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A 
       12.20         5.13        36.07         4.34         5.13         7.99 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        9.90        38.63         1.08        27.12        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84         9.99         6.48         8.68        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        9.67        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        33.83        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        1.15        34.98         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51         9.53        29.46         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MU 
      111.78       111.91        56.02        25.08        29.65         5.56 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       21.60        16.14         0.46        13.94        33.60        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E 
       12.95        38.40         5.72        76.41         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
       11.11       114.15         4.21        13.45        42.84        34.68 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       36.07        78.44        11.80         1.51        13.08         9.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
        6.58         1.71         6.71         3.58         5.36        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        7.30         3.39        20.38        19.53         7.17        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       12.89        47.38        52.08         8.81        49.15         8.68 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
        0.82         5.23        53.85         3.22         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY 
       14.20        10.78         6.41         0.20         0.99         0.43 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        9.90        12.85        31.33        84.72        10.13        16.24 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        14.70        11.84        10.65        11.05         5.79 

  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                        122.73                         124.31 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                        15.945                         13.875 
[1] "0.0 - 122.7 (15.9)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1.2"
D54V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(19P13.3) MUTATED    38  42
  DEL PEAK 31(19P13.3) WILD-TYPE 104  92
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            80                            196 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            42                             92 
$`DEL PEAK 31(19P13.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JL 
       16.57        31.59        95.74        43.43        11.87       171.58 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A148 TCGA-D9-A3Z3 TCGA-D9-A6EA 
       15.06       110.93       135.75       151.53         3.25        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       48.89        36.03        20.38       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL 
       65.92        68.09       215.44        10.16        35.01         3.55 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
       29.82         4.96       168.26        13.55        47.84        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       72.07        32.19        18.61        25.87        17.92        46.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MG 
       58.75        47.54        75.48        55.59        94.82       103.20 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
      248.65        43.23       136.47        41.59       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A193 
        3.68       127.20        36.95        53.19        27.35        31.40 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19W 
       98.40        48.89       152.35        61.05        50.89       148.18 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       23.34        31.27        32.05        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT 
        4.90        53.52        15.45        32.75       133.55        53.16 
TCGA-FS-A1ZW TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO 
       49.48        26.73        77.88        47.54         0.16         7.23 
TCGA-GN-A262 TCGA-GN-A268 
      120.46        62.79 

$`DEL PEAK 31(19P13.3) WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       90.90       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       69.90        48.76       113.52        42.08        12.10        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR 
      131.90        18.38        10.03        51.68       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
        7.43       125.19        54.67         3.65         6.41        11.34 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        66.25        22.95       117.21       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       35.93        23.44        28.60        10.49        15.68        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y 
       17.85        45.11        52.01         6.35        12.20        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E 
      109.64       151.27        78.87        63.35        80.61        39.62 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        2.60        44.35        56.42        37.35        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
      345.96       171.55       102.90        24.43        39.29        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       79.66        90.97       101.95        13.91        14.30        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
      167.90        47.54       103.56        53.26       124.31        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        23.47       138.81       172.18        64.08        34.32 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       33.40       101.79       148.08        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        12.59        13.02        26.37       268.93 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 
        6.44       131.51        44.05       162.08        37.25        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       43.82        20.15        16.37       247.04        80.32        33.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
      210.08        15.16         7.00       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
      357.37        40.27         9.70        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       74.73        11.41       148.80        26.56        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        12.43 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       49.45         0.20        22.92         2.40         9.90        14.04 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        10.13        64.44        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                          0.16                           0.20 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                        248.65                         357.37 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                        47.690                         48.065 
[1] "0.2 - 248.7 (47.7)" "0.2 - 357.4 (48.1)"
[1] "hr=" "1.3"
D54V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 31(19P13.3) MUTATED                   11             1
  DEL PEAK 31(19P13.3) WILD-TYPE                 26             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 31(19P13.3) MUTATED                                          13
  DEL PEAK 31(19P13.3) WILD-TYPE                                        47
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 31(19P13.3) MUTATED                    56
  DEL PEAK 31(19P13.3) WILD-TYPE                 123
D54V4, multiclass
                                           clus
vv                                          DEL PEAK 31(19P13.3) MUTATED
  DISTANT METASTASIS                                                  11
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           13
  REGIONAL LYMPH NODE                                                 56
                                           clus
vv                                          DEL PEAK 31(19P13.3) WILD-TYPE
  DISTANT METASTASIS                                                    26
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             47
  REGIONAL LYMPH NODE                                                  123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 31(19P13.3) MUTATED             4       0       5        4        8
  DEL PEAK 31(19P13.3) WILD-TYPE           6       6      18        6       17
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 31(19P13.3) MUTATED          3         2         3         2
  DEL PEAK 31(19P13.3) WILD-TYPE       14         8        11         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 31(19P13.3) MUTATED          12          2         10         14
  DEL PEAK 31(19P13.3) WILD-TYPE        20         12         13         34
                                vv
clus                             STAGE IV
  DEL PEAK 31(19P13.3) MUTATED          4
  DEL PEAK 31(19P13.3) WILD-TYPE        8
D54V5, multiclass
             clus
vv            DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  I OR II NOS                            4                              6
  STAGE 0                                0                              6
  STAGE I                                5                             18
  STAGE IA                               4                              6
  STAGE IB                               8                             17
  STAGE II                               3                             14
  STAGE IIA                              2                              8
  STAGE IIB                              3                             11
  STAGE IIC                              2                              8
  STAGE III                             12                             20
  STAGE IIIA                             2                             12
  STAGE IIIB                            10                             13
  STAGE IIIC                            14                             34
  STAGE IV                               4                              8
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 31(19P13.3) MUTATED      17 20 13 15
  DEL PEAK 31(19P13.3) WILD-TYPE    36 40 42 42
D54V6, multiclass
       clus
vv      DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  T0+T1                           17                             36
  T2                              20                             40
  T3                              13                             42
  T4                              15                             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 31(19P13.3) MUTATED    37  14  13  12
  DEL PEAK 31(19P13.3) WILD-TYPE 104  37  19  25
D54V7, multiclass
    clus
vv   DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  N0                           37                            104
  N1                           14                             37
  N2                           13                             19
  N3                           12                             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B M1C
  DEL PEAK 31(19P13.3) MUTATED    71   0   1   1   3
  DEL PEAK 31(19P13.3) WILD-TYPE 181   4   1   1   2
D54V8, multiclass
     clus
vv    DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  M0                            71                            181
  M1                             0                              4
  M1A                            1                              1
  M1B                            1                              1
  M1C                            3                              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   33 19
  DEL PEAK 31(19P13.3) WILD-TYPE 71 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     33   19
  DEL PEAK 31(19P13.3) WILD-TYPE   71   53
     clus
vv    DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  NO                            33                             71
  YES                           19                             53
[1] 2 2
[1] FALSE
D54V10, binary
                                cls
clus                               0   1
  DEL PEAK 31(19P13.3) MUTATED     9  72
  DEL PEAK 31(19P13.3) WILD-TYPE  25 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED      9   72
  DEL PEAK 31(19P13.3) WILD-TYPE   25  175
     clus
vv    DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  NO                             9                             25
  YES                           72                            175
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, binary
                                cls
clus                               0   1
  DEL PEAK 31(19P13.3) MUTATED    36  45
  DEL PEAK 31(19P13.3) WILD-TYPE  72 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     36   45
  DEL PEAK 31(19P13.3) WILD-TYPE   72  128
        clus
vv       DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  FEMALE                           36                             72
  MALE                             45                            128
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(19P13.3) MUTATED       1                         0    80
  DEL PEAK 31(19P13.3) WILD-TYPE     4                         1   195
D54V13, multiclass
                           clus
vv                          DEL PEAK 31(19P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               80
                           clus
vv                          DEL PEAK 31(19P13.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                                cls
clus                               0   1
  DEL PEAK 31(19P13.3) MUTATED     0  80
  DEL PEAK 31(19P13.3) WILD-TYPE   3 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED      0   80
  DEL PEAK 31(19P13.3) WILD-TYPE    3  194
                        clus
vv                       DEL PEAK 31(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           80
                        clus
vv                       DEL PEAK 31(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            194
[1] 2 2
[1] FALSE
