[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/11541723/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/11573325/transformed.cor.cli.txt"

nPatients in clinical file=349, in cluster file=366, common to both=348
[1]  55 348
[1] "AMP PEAK  1(1P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                        117                         231 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                        117                         231 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          192                           156 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          192                           156 
[1] "AMP PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        191                         157 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        191                         157 
[1] "AMP PEAK  4(3P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         99                         249 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         99                         249 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         63                         285 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         63                         285 
[1] "AMP PEAK  6(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           106                            242 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           106                            242 
[1] "AMP PEAK  7(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           57                           291 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           57                           291 
[1] "AMP PEAK  8(6P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          199                           149 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          199                           149 
[1] "AMP PEAK  9(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         76                         272 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         76                         272 
[1] "AMP PEAK 10(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          195                           153 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          195                           153 
[1] "AMP PEAK 11(7Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        213                         135 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        213                         135 
[1] "AMP PEAK 12(8Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                           156                            192 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                           156                            192 
[1] "AMP PEAK 13(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           181                            167 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           181                            167 
[1] "AMP PEAK 14(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            66                            282 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            66                            282 
[1] "AMP PEAK 15(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                            54                            294 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                            54                            294 
[1] "AMP PEAK 16(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          55                          293 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          55                          293 
[1] "AMP PEAK 17(13Q31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                           100                            248 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                           100                            248 
[1] "AMP PEAK 18(15Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                           116                            232 
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                           116                            232 
[1] "AMP PEAK 19(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                           118                            230 
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                           118                            230 
[1] "AMP PEAK 20(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            67                            281 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            67                            281 
[1] "AMP PEAK 21(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                            182                             166 
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                            182                             166 
[1] "AMP PEAK 22(22Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                           145                            203 
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                           145                            203 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            80                            268 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            80                            268 
[1] "DEL PEAK  2(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           91                           257 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           91                           257 
[1] "DEL PEAK  3(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           89                           259 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           89                           259 
[1] "DEL PEAK  4(3P25.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           67                           281 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           67                           281 
[1] "DEL PEAK  5(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            57                            291 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            57                            291 
[1] "DEL PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           86                           262 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           86                           262 
[1] "DEL PEAK  7(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          103                           245 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          103                           245 
[1] "DEL PEAK  8(5P15.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            75                            273 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            75                            273 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           93                           255 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           93                           255 
[1] "DEL PEAK 10(5Q31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                          124                           224 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                          124                           224 
[1] "DEL PEAK 11(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                           202                            146 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                           202                            146 
[1] "DEL PEAK 12(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        209                         139 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        209                         139 
[1] "DEL PEAK 13(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           82                           266 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           82                           266 
[1] "DEL PEAK 14(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        237                         111 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        237                         111 
[1] "DEL PEAK 15(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          266                            82 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          266                            82 
[1] "DEL PEAK 16(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           191                            157 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           191                            157 
[1] "DEL PEAK 17(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           208                            140 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           208                            140 
[1] "DEL PEAK 18(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            219                             129 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            219                             129 
[1] "DEL PEAK 19(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           225                            123 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           225                            123 
[1] "DEL PEAK 20(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           110                            238 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           110                            238 
[1] "DEL PEAK 21(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           192                            156 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           192                            156 
[1] "DEL PEAK 22(12Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            87                            261 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            87                            261 
[1] "DEL PEAK 23(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          79                          269 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          79                          269 
[1] "DEL PEAK 24(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           116                            232 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           116                            232 
[1] "DEL PEAK 25(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                            115                             233 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                            115                             233 
[1] "DEL PEAK 26(15Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            81                            267 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            81                            267 
[1] "DEL PEAK 27(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            87                            261 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            87                            261 
[1] "DEL PEAK 28(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            60                            288 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            60                            288 
[1] "DEL PEAK 29(16Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                           111                            237 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                           111                            237 
[1] "DEL PEAK 30(16Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                           125                            223 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                           125                            223 
[1] "DEL PEAK 31(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                           131                            217 
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                           131                            217 
[1] "DEL PEAK 32(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            98                            250 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            98                            250 
[1] "DEL PEAK 33(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                           84                           264 
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                           84                           264 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DAYSTOSUBMITTEDSPECIMENDX"             
 [6] "PRIMARYSITEOFDISEASE"                  
 [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 348 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
          NA         1856           NA           NA           NA         3408 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
          NA           NA         4053           NA           NA         2765 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
        2912           NA           NA           NA           NA         3514 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
          NA         2639           NA         1888           NA         1280 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
          NA         5219         1709         2010         1812         3976 
TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
          NA           NA           NA         1429         1409         5065 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
        2644           NA           NA           NA           NA         3151 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51G TCGA-D3-A51H 
        1209         1378         5318         1695           NA         1714 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
        4414         1002          688         1941          818         3826 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
        4129         4195         5424          553         3808           NA 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
          NA          353          462           NA         6965         5177 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GO TCGA-D3-A8GP TCGA-D3-A8GQ 
          NA         2897         4897           NA         4191           NA 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
          NA           NA         4609         1663          111          195 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
         551          345          678          338          301          766 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2015           NA         1487           NA         3565           NA 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        5926           NA           NA         3265         1861           NA 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
          NA          713           NA          870           NA         6553 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
         477          422          309          543         2076         1643 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
         526         1582          193          371           NA           NA 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
          NA         4070           NA         2785           NA           NA 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
          NA         2452         1455           NA         1940           NA 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        1966           NA         1729           NA         1716         1136 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
         440         1701        11252           NA         5932           NA 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
          NA         3130         1120           NA         2620         1803 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
        2051         9568         4898         6328         1482         2717 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
        1665         2423         2296         2767         3857           NA 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
         435         1691         1365         2884           NA         3932 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
          NA           NA           NA           NA         4825         6176 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
          NA           NA         7563           NA         4088         4942 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
        2166         1620         3781         3733         1570          112 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        1658           NA          714           NA           NA           NA 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
          NA         1949           NA           NA         6138           NA 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        1562         3333         4504           NA           NA           NA 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
          NA           NA         2365           NA           NA           NA 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
          NA           NA         8180           NA           NA           NA 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
          NA         1340           NA           NA           NA         1133 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
          NA           NA         2433           NA           NA           NA 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
         498          951          975           NA         2443         1429 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FR-A69P 
        1010          206         2828           NA         5299          478 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
        6390          461          213         1164           NA          896 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        2871           NA           NA           NA           NA           NA 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        1225           NA           NA           NA           NA           NA 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
        3080           NA           NA           NA         4526         1617 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
          NA         1505           NA           NA         2367           NA 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
          NA           NA           NA          378           NA         1504 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2369            6          697         1446            5          587 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
         301          220           62          357         4255           NA 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        2577           NA           NA           NA           NA         1204 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
        1410          384           NA           NA           NA           NA 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
          NA        10860         8966          203           NA           10 
TCGA-RP-A694 TCGA-RP-A695 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
          21           NA         6455           NA           NA           NA 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
          NA         6666           NA          731         1173         1654 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
         262         2746         1733         1807         1592          114 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
         690         1330           67          918          315          461 
TCGA-YD-A9TB TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
          NA         1096          439          719         2831          357 
Variable 1:'AGE':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=165,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=189,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=274,	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=124,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=31,	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=21,	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 348 columns, 2 survival variables, and 12 non-survival variables.
AGE, nv=68, 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 
23 40 71 74 67 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   63    71    74    67 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 40 71 74 67 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   63    71    74    67 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
168  61  38  47 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
168  61  38  47 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
168  61  38  47 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
168  61  38  47 
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=124, 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    51  61
  AMP PEAK  1(1P12) WILD-TYPE 117 104
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                        112                         221 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         61                         104 
$`AMP PEAK  1(1P12) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A2J6 TCGA-D3-A2JA 
        3.02         6.97        16.47         8.52        10.29        88.50 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
       86.76        11.41        92.42        64.44       114.67        15.25 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GO 
        6.31         9.34       103.59        93.21        32.61        47.87 
TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM 
       17.72        22.06        10.22         4.18       142.45        75.65 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       11.44         5.56         4.01        21.93         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
       13.22         7.00         0.20        13.35        13.22         0.20 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I 
        8.12         1.12        12.20         4.31        60.23         1.18 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15        62.79         8.55         1.08        39.62 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GJ 
        2.43        32.15         8.09        51.12        30.08        19.43 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ 
       35.54         5.42         1.15         9.53        14.56        63.42 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD 
       56.02        21.60        60.49         5.56       122.73         3.68 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19D 
       15.95         3.22        21.60        22.22         5.72         3.52 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3ET 
       11.90       114.15        13.45         6.58         1.87         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 
        1.71        18.41        85.74        15.72         6.71         5.36 
TCGA-FR-A7UA TCGA-FS-A1YX TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZU 
       13.28         3.45        30.87        12.89         8.65         8.68 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
        3.22        28.73         0.20         7.23        11.61        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-HR-A2OH TCGA-QB-AA9O TCGA-W3-A825 
       10.13        16.24        12.16        15.81        18.05         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZQ TCGA-WE-A8ZY 
       60.03         2.99       185.16         5.49         3.72         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
        1.08        19.96         1.94         6.18 

$`AMP PEAK  1(1P12) WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        6.97       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        81.24        85.32         8.38        21.14 
TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       68.22        44.19         7.50        36.16         6.31        56.19 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       59.57        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       24.00        26.37        29.23        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       32.28        21.44        25.78       110.24        52.01        13.68 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       23.11        29.72        15.19       108.79        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       87.62        24.07         5.72        14.60        48.79        35.80 
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-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-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.13        23.15        19.00 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C 
       11.57        10.55         6.31         1.35         5.13         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29N 
       15.85         9.21         7.99         9.90        36.85         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 
       12.03         8.09         8.84         9.99        30.44        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       60.00        47.21        16.01        28.31        33.83        55.69 
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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51        29.46         2.73        44.25         7.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      125.65       111.91        25.08        26.99        53.16        52.67 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
      124.31        51.62        30.15        13.81        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14         0.95        27.35        18.41        21.73 
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-A19C TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       25.18         3.78        11.11        34.88         4.21        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-ER-A3EV TCGA-ER-A42K TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       22.49         5.62         3.58         2.20         4.70         3.29 
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-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-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.17        12.92        47.38        52.08         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       14.20        10.78         5.98         6.41         2.27         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
        0.13         0.16        17.33         9.90         0.85        44.28 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       84.72        15.42        14.70        11.84        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       14.50        14.50         0.43        11.05         5.79         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 
        0.69       164.19        10.98        71.01        11.84         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
        7.10        18.67        21.07        13.12         3.42        21.83 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         4.70         8.22         6.67         5.98 

  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                       0.20                        0.13 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                     185.16                      164.19 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                     11.755                      17.720 
[1] "0.2 - 185.2 (11.8)" "0.1 - 164.2 (17.7)"
[1] "hr=" "1.4"
D1V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  1(1P12) MUTATED    52  61
  AMP PEAK  1(1P12) WILD-TYPE 121 105
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                        113                         226 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         61                         105 
$`AMP PEAK  1(1P12) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A2J6 TCGA-D3-A2JA 
       17.03        12.99        16.57        16.67        43.43       115.53 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
       86.76        11.87       171.58        66.08       130.72        58.06 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GO 
       13.87         9.34       103.59       174.84        63.81       137.92 
TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM 
       18.18        79.59        11.61        58.52       228.99        95.24 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       29.06       129.63        18.12        11.34        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN 
       25.18        66.25        10.49        10.16        17.29        52.01 
TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       12.20        94.98        33.73        26.89         4.96       133.81 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       13.55        47.84        13.97        63.78        72.07         2.60 
TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GI 
       56.84        25.87       195.02        17.92        59.28        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MD TCGA-EE-A2MI 
       89.33        79.66        13.91        14.30        47.28       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB 
       96.23       167.90        43.23       134.40        53.26       122.73 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 
        3.68        23.47       172.18        64.08        53.19         9.17 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A2ND 
       12.59        13.02       268.93       131.51         8.88        23.34 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       80.32        33.21        92.98       174.21        15.72       210.08 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FS-A1YX TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZQ 
        7.00        38.27        48.59        32.75        23.93       133.55 
TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 
       26.56        50.14        28.73         0.20         7.23        11.74 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-HR-A2OH TCGA-QB-AA9O 
      117.93        10.13        64.44        32.48        65.88        18.05 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZQ 
       63.02       121.08         4.01       219.16        38.56        52.34 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        36.03 

$`AMP PEAK  1(1P12) WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       61.02       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74       103.10        65.49        23.77 
TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
      168.00        62.07       113.52        42.08        12.10        56.19 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       59.57        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       24.53        39.75        45.30        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       32.94        22.62        26.89       125.79       135.75       178.32 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
      125.19        30.84        15.19       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      137.79       117.17       151.53        54.67         3.65         6.41 
TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.11        22.95        48.89        36.03       117.21        20.38 
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-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       65.92        23.44        68.09        28.60       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X 
       13.87        17.85        68.25        54.02         6.35        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F 
       27.22         8.65        14.70        68.15       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
      168.26        63.35        80.61        64.64        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 
       37.35        14.47        55.92       369.93        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        67.43       314.56       161.03 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS 
      208.04        54.74        75.48        90.97       126.81        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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       61.51       103.27       268.73       103.20        16.96       158.63 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      203.05        47.54       248.65       162.48        71.21       124.31 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       51.62        54.51        13.81       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32       201.80        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        35.44        13.94        50.76        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       48.89        26.37       152.35         6.44        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-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-ER-A42K TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        6.77        15.16        34.82        29.46        94.39       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-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38       101.26        74.73        11.41       148.80        53.16 
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-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
        0.16        19.30         9.90         2.04       139.89        84.72 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       62.79        39.58        46.36        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       59.41       357.04       294.77         6.67         0.33         0.69 
TCGA-W3-A824 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
      212.22        42.08       105.04        24.03        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA4 
       90.28        56.98        59.41         3.75        22.68        15.16 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  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                      369.93 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                      43.23                       53.97 
[1] "0.2 - 268.9 (43.2)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.4"
D1V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  1(1P12) MUTATED                   19             4
  AMP PEAK  1(1P12) WILD-TYPE                 42             1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  1(1P12) MUTATED                                          26
  AMP PEAK  1(1P12) WILD-TYPE                                        46
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  1(1P12) MUTATED                    68
  AMP PEAK  1(1P12) WILD-TYPE                 141
D1V4, multiclass
                                           clus
vv                                          AMP PEAK  1(1P12) MUTATED
  DISTANT METASTASIS                                               19
  PRIMARY TUMOR                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        26
  REGIONAL LYMPH NODE                                              68
                                           clus
vv                                          AMP PEAK  1(1P12) WILD-TYPE
  DISTANT METASTASIS                                                 42
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          46
  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
  AMP PEAK  1(1P12) MUTATED             5       4       5        6       11
  AMP PEAK  1(1P12) WILD-TYPE           7       3      23       11       16
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  1(1P12) MUTATED         12         4         4         4        10
  AMP PEAK  1(1P12) WILD-TYPE       10        10        15         8        25
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  1(1P12) MUTATED           10          8         21        6
  AMP PEAK  1(1P12) WILD-TYPE          5         24         37       13
D1V5, multiclass
             clus
vv            AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  I OR II NOS                         5                           7
  STAGE 0                             4                           3
  STAGE I                             5                          23
  STAGE IA                            6                          11
  STAGE IB                           11                          16
  STAGE II                           12                          10
  STAGE IIA                           4                          10
  STAGE IIB                           4                          15
  STAGE IIC                           4                           8
  STAGE III                          10                          25
  STAGE IIIA                         10                           5
  STAGE IIIB                          8                          24
  STAGE IIIC                         21                          37
  STAGE IV                            6                          13
[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      17 22 30 24
  AMP PEAK  1(1P12) WILD-TYPE    46 49 44 43
D1V6, multiclass
       clus
vv      AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  T0+T1                        17                          46
  T2                           22                          49
  T3                           30                          44
  T4                           24                          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  1(1P12) MUTATED    58  18  14  18
  AMP PEAK  1(1P12) WILD-TYPE 110  43  24  29
D1V7, multiclass
    clus
vv   AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  N0                        58                         110
  N1                        18                          43
  N2                        14                          24
  N3                        18                          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  1(1P12) MUTATED   103   1   2   0   3
  AMP PEAK  1(1P12) WILD-TYPE 203   3   1   4   6
D1V8, multiclass
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  M0                        103                         203
  M1                          1                           3
  M1A                         2                           1
  M1B                         0                           4
  M1C                         3                           6
[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   47 27
  AMP PEAK  1(1P12) WILD-TYPE 82 60
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     47   27
  AMP PEAK  1(1P12) WILD-TYPE   82   60
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  NO                         47                          82
  YES                        27                          60
[1] 2 2
[1] FALSE
D1V10, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED    14 103
  AMP PEAK  1(1P12) WILD-TYPE  29 201
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     14  103
  AMP PEAK  1(1P12) WILD-TYPE   29  201
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  NO                         14                          29
  YES                       103                         201
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, binary
                             cls
clus                            0   1
  AMP PEAK  1(1P12) MUTATED    43  74
  AMP PEAK  1(1P12) WILD-TYPE  88 143
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED     43   74
  AMP PEAK  1(1P12) WILD-TYPE   88  143
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  FEMALE                        43                          88
  MALE                          74                         143
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P12) MUTATED       2                         0   107
  AMP PEAK  1(1P12) WILD-TYPE     3                         1   219
D1V13, multiclass
                           clus
vv                          AMP PEAK  1(1P12) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                           107
                           clus
vv                          AMP PEAK  1(1P12) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             219
[1] 3 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     3 112
  AMP PEAK  1(1P12) WILD-TYPE   4 222
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      3  112
  AMP PEAK  1(1P12) WILD-TYPE    4  222
                        clus
vv                       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  HISPANIC OR LATINO                             3                           4
  NOT HISPANIC OR LATINO                       112                         222
[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   91 94
  AMP PEAK  2(1Q21.3) WILD-TYPE 77 71
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          185                           148 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           94                            71 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 
        3.02         6.97         6.97        16.47         8.52       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       28.08        81.24         8.38        21.14        88.50        86.76 
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE 
       11.41        92.42        56.19       114.67        15.25        13.32 
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        29.23        93.21 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       32.28        32.61        52.01        47.87        17.72        23.11 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       22.06        10.22         4.18       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       75.65        87.62        11.44         5.56         4.01        21.93 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        11.31        13.22        14.60        10.03        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 
        9.99        44.52        36.69         4.93         6.64         7.00 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
       17.56         0.20        19.00        13.35        13.22         0.20 
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-A20H TCGA-EE-A20I TCGA-EE-A29B 
        5.13         4.31        60.23         9.21         1.18         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R 
       11.15        62.79         8.55         1.08        39.62         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        9.99        30.44        32.15        49.22        36.30        36.33 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       51.12        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU 
       35.54        28.31        33.83        55.69        13.02        36.33 
TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
        2.70        63.42        25.08        21.60        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG 
       52.67         5.56       122.73        51.62         3.68        15.95 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 
        3.22        21.60        21.60        22.22        21.73        12.95 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        5.72         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL 
        9.57         6.58         1.87        12.62        22.49         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 
        5.62        18.41        85.74        15.72         6.71         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
       13.28         2.20         4.70        64.47         3.45        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
       14.24         7.30        20.38         8.22        11.08        30.87 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
       12.89        52.08         8.65        40.64         8.68         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A6C8 
        5.23        53.85        28.73         2.27         0.20         0.85 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        16.24        12.16        14.70        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       14.50        14.50        14.50        15.81         0.43         5.79 
TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 
        0.69         8.98        60.03         2.99       185.16        71.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       11.84         5.49         6.48        13.12         3.72        21.83 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36        19.96         1.94        12.07         6.18 

$`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        44.19         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        59.57        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        54.74        31.30        54.31        21.44        25.78 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS 
      110.24        13.68        29.72        15.19       124.47        24.07 
TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I8 
        5.72        48.79        35.80        51.12        13.68        25.15 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       22.36        19.36        14.83        13.15         0.13        23.15 
TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H 
       11.57         4.34        15.85         7.99        37.97        36.85 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
        9.50        12.03         8.09         2.43         8.09        11.31 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
        9.67        34.29        16.01         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73        44.25         7.96        14.56       125.65       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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       22.92        16.14         0.95        27.35        18.41        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       31.40        18.61        38.40        76.41        25.18         3.78 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
        4.21        13.45        28.60        42.84        34.68        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       17.72        78.44        11.80         1.51        13.08        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z4 
        9.04         6.58         3.58         3.29        11.01        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
        7.33         3.39        19.53         7.17        12.92        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-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       10.78         5.98         6.41         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       17.33         9.90         7.23        11.61        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A268 TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 
       84.72        15.42        11.05        18.05         0.33       164.19 
TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZT TCGA-WE-AA9Y 
       10.98         7.10        18.67        21.07         3.42         1.08 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.20                          0.13 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       185.16                        164.19 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       13.350                        16.075 
[1] "0.2 - 185.2 (13.3)" "0.1 - 164.2 (16.1)"
[1] "hr=" "1.1"
D2V2, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   92 95
  AMP PEAK  2(1Q21.3) WILD-TYPE 81 71
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          187                           152 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           95                            71 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 
       17.03        61.02        12.99        16.57        16.67       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       28.08        95.74        65.49        23.77       115.53        86.76 
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE 
       11.87       171.58        56.19       130.72        58.06        60.23 
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        45.30       174.84 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       32.94        63.81       135.75       137.92        18.18       125.19 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        11.61        58.52       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX 
       95.24       137.79        29.06       129.63         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       11.34        22.29         9.90        25.18        66.25        22.95 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       20.38       194.83        35.93       107.34        61.18        65.92 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL 
       68.09        10.49       215.44        10.16        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       52.01        12.20        27.22         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       133.81       168.26 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       13.55        80.61        13.97        63.78        72.07         2.60 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       56.84        14.47        55.92       369.93       195.02       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.82        86.14        59.28       314.56       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        89.33        79.66        75.48        90.97       126.81 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ 
       55.59        94.82        28.83        96.23        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40       162.48        71.21        53.26       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
        3.68        23.47       172.18        36.95        64.08        53.19 
TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
      109.58        13.94         9.17        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG 
      268.93       152.35        50.89         8.88        23.34        31.27 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
      210.08         7.00        38.27        34.82        29.46       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         2.04        10.13        64.44        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       46.36        12.62        50.10        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
      357.04         6.67         0.69        63.02       121.08         4.01 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO 
      219.16       105.04        24.03        38.56        54.38        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       52.34        22.68        43.73        30.18        10.36        15.16 
TCGA-YG-AA3O 
       36.03 

$`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        62.07       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        59.57        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        55.73        56.35       145.12        22.62        26.89 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS 
      125.79       178.32        30.84        15.19       161.00       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW 
      151.53        54.67        18.12        11.11        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        68.25         6.35        29.82       151.27 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       91.56        63.35        47.84        64.64        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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       16.96       204.66       158.63       203.05       167.90       248.65 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 
      124.31        54.51        13.81       138.81       127.20        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       148.08        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19L 
       50.76        77.75        98.40        48.89         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05       162.08        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       43.82        20.15        16.37        32.05       247.04        80.32 
TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
       15.16        94.39       228.59        28.08         7.79        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       40.27         9.70        47.38       101.26        11.41       148.80 
TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       49.48        50.14        66.67       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        7.23        11.74       139.89       117.93        84.72        62.79 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8K6 
      294.77        18.05         0.33       212.22        42.08         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-YG-AA3P TCGA-Z2-A8RT 
       90.28        56.98         3.75         2.20        14.43        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  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 
                       369.93                        294.77 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       51.620                        49.465 
[1] "0.2 - 369.9 (51.6)" "0.2 - 294.8 (49.5)"
[1] "hr=" "1.1"
D2V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  2(1Q21.3) MUTATED                   42             4
  AMP PEAK  2(1Q21.3) WILD-TYPE                 19             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  2(1Q21.3) MUTATED                                          39
  AMP PEAK  2(1Q21.3) WILD-TYPE                                        33
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK  2(1Q21.3) MUTATED                   106
  AMP PEAK  2(1Q21.3) WILD-TYPE                 103
D2V4, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  DISTANT METASTASIS                                                 42
  PRIMARY TUMOR                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          39
  REGIONAL LYMPH NODE                                               106
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  DISTANT METASTASIS                                                   19
  PRIMARY TUMOR                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            33
  REGIONAL LYMPH NODE                                                 103
[1] 4 2
[1] 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             5       4      10       10       19
  AMP PEAK  2(1Q21.3) WILD-TYPE           7       3      18        7        8
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  2(1Q21.3) MUTATED         14         9        10         8
  AMP PEAK  2(1Q21.3) WILD-TYPE        8         5         9         4
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  2(1Q21.3) MUTATED          19         11         18         29
  AMP PEAK  2(1Q21.3) WILD-TYPE        16          4         14         29
                               vv
clus                            STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED         13
  AMP PEAK  2(1Q21.3) WILD-TYPE        6
D2V5, multiclass
             clus
vv            AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  I OR II NOS                           5                             7
  STAGE 0                               4                             3
  STAGE I                              10                            18
  STAGE IA                             10                             7
  STAGE IB                             19                             8
  STAGE II                             14                             8
  STAGE IIA                             9                             5
  STAGE IIB                            10                             9
  STAGE IIC                             8                             4
  STAGE III                            19                            16
  STAGE IIIA                           11                             4
  STAGE IIIB                           18                            14
  STAGE IIIC                           29                            29
  STAGE IV                             13                             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  2(1Q21.3) MUTATED      36 40 44 39
  AMP PEAK  2(1Q21.3) WILD-TYPE    27 31 30 28
D2V6, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T0+T1                          36                            27
  T2                             40                            31
  T3                             44                            30
  T4                             39                            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  2(1Q21.3) MUTATED   94 30 24 26
  AMP PEAK  2(1Q21.3) WILD-TYPE 74 31 14 21
D2V7, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          94                            74
  N1                          30                            31
  N2                          24                            14
  N3                          26                            21
[1] 4 2
[1] 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   170   2   3   1   7
  AMP PEAK  2(1Q21.3) WILD-TYPE 136   2   0   3   2
D2V8, multiclass
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  M0                          170                           136
  M1                            2                             2
  M1A                           3                             0
  M1B                           1                             3
  M1C                           7                             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"
D2V9, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   77 50
  AMP PEAK  2(1Q21.3) WILD-TYPE 52 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     77   50
  AMP PEAK  2(1Q21.3) WILD-TYPE   52   37
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           77                            52
  YES                          50                            37
[1] 2 2
[1] FALSE
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    22 169
  AMP PEAK  2(1Q21.3) WILD-TYPE  21 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     22  169
  AMP PEAK  2(1Q21.3) WILD-TYPE   21  135
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           22                            21
  YES                         169                           135
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    74 118
  AMP PEAK  2(1Q21.3) WILD-TYPE  57  99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     74  118
  AMP PEAK  2(1Q21.3) WILD-TYPE   57   99
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          74                            57
  MALE                           118                            99
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q21.3) MUTATED       3                         0   178
  AMP PEAK  2(1Q21.3) WILD-TYPE     2                         1   148
D2V13, multiclass
                           clus
vv                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             178
                           clus
vv                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               148
[1] 3 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     5 183
  AMP PEAK  2(1Q21.3) WILD-TYPE   2 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      5  183
  AMP PEAK  2(1Q21.3) WILD-TYPE    2  151
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         183
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           151
[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   94 90
  AMP PEAK  3(1Q44) WILD-TYPE 74 75
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        184                         149 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         90                          75 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
        3.02        16.47         8.52       110.79        28.08        81.24 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL 
        8.38        21.14        88.50        86.76        11.41        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
       56.19        64.44       114.67        15.25        46.98        13.32 
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        29.23        93.21 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       32.28        32.61       110.24        52.01        47.87        17.72 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.11        10.22         4.18       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       75.65        87.62        11.44         5.56         4.01        21.93 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        13.22        14.60        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       39.19         9.99        44.52        36.69         4.93         6.64 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
        7.00        17.56         0.20        19.00        13.35        13.22 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        0.20        10.55         8.12         1.12         1.35         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D 
        4.31        60.23         9.21         1.18         9.90        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29R 
       62.79         8.55         1.08        39.62        12.03         8.84 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       30.44        32.15        49.22        36.30        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       17.98        60.00        47.21        30.08        19.43        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MF 
       33.83        55.69        13.02        36.33         2.70         2.73 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16        52.67         5.56       122.73        51.62         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        21.73 
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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z0 
       85.74        15.72         6.71         2.20         3.45        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       14.24        20.38        11.08        30.87        12.92        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-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A266 
       53.85        28.73         6.41         2.27         0.20        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       16.24        12.16        14.70        11.84        10.65        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 
       14.50        15.81         0.43         5.79        18.05         0.69 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        8.98        60.03         2.99       185.16        71.01        11.84 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY 
        5.49         7.10        13.12         3.72        21.83         5.36 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       19.96         1.94        12.07         6.18 

$`AMP PEAK  3(1Q44) WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
        6.97         6.97       111.09        32.42        70.16        22.55 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG 
       45.83        10.29        85.32        68.22        44.19         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       36.16         6.31        59.57        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        54.74        31.30        54.31        21.44        25.78 
TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS 
       13.68        29.72        22.06        15.19       124.47        24.07 
TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB 
        5.72        48.79        35.80        13.68        25.15        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EE-A17X 
       19.36        14.83        13.15         0.13        23.15        11.57 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
        6.31        12.20         4.34        15.85         7.99        37.97 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       36.85         9.50         8.09         9.99         2.43         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
       11.31         9.67        34.29        16.01        35.54         5.42 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
        1.15        34.98         8.84        98.27         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
        9.53        29.46        44.25         7.96        14.56       125.65 
TCGA-EE-A2MM TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 
       56.02       124.31        30.15        13.81        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 
       16.14         0.95        27.35        18.41        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19J 
       18.61        38.40        76.41        25.18        11.90         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       13.45        28.60        42.84        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A7U8 TCGA-FR-A7U9 
       78.44        11.80         1.51        12.62         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 
       13.28         4.70         3.29        64.47        11.01        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.33         7.30         3.39         8.22        19.53         7.17 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 
       47.38         8.81        49.15        27.39         3.22         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       14.20        10.78         5.98         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A693 
       31.33        84.72        15.42        14.50        11.05         0.33 
TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZT 
      164.19        10.98         6.48        18.67        21.07         3.42 
TCGA-WE-AA9Y TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.08         4.70         8.22         6.67         5.98 

  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                       0.20                        0.13 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     185.16                      164.19 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                      14.55                       15.19 
[1] "0.2 - 185.2 (14.6)" "0.1 - 164.2 (15.2)"
[1] "hr=" "1.1"
D3V2, survival
                             sevent
clus2                          0  1
  AMP PEAK  3(1Q44) MUTATED   95 91
  AMP PEAK  3(1Q44) WILD-TYPE 78 75
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                        186                         153 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         91                          75 
$`AMP PEAK  3(1Q44) MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       17.03        16.57        16.67       133.25        28.08        95.74 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL 
       65.49        23.77       115.53        86.76        11.87       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
       56.19        66.08       130.72        58.06        46.98        60.23 
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        45.30       174.84 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       32.94        63.81       125.79       135.75       137.92        18.18 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      125.19        11.61        58.52       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX 
       95.24       137.79        29.06       129.63         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       11.34        22.29         9.90        25.18        66.25        22.95 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       194.83        35.93       107.34        61.18 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH 
       65.92        68.09        10.49       215.44        10.16        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       17.29        52.01        12.20        27.22        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I 
       14.70        68.15         4.96       133.81       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        63.78        72.07         2.60        56.84 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       56.42        14.47       369.93       195.02       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28       314.56       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU 
       89.33        75.48        90.97       126.81        55.59        94.82 
TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       28.83       268.73        96.23       203.05        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       43.23       134.40       162.48        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       51.62         3.68        23.47       138.81       172.18        64.08 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       53.19       109.58        13.94         9.17        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND 
       26.37       268.93       152.35       162.08        50.89        23.34 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC 
        6.77        92.98       174.21        15.72       210.08        34.82 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH 
       48.59       202.65        20.91       357.37        15.45        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        23.93        74.73       133.55        53.16        26.56 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FS-A4FD 
       27.09        27.02        77.82        28.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
        0.20        10.13        64.44        32.48        39.58        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       12.62        50.10        59.41        65.88       357.04         6.67 
TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
       18.05         0.69        63.02       121.08         4.01       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      105.04        24.03        38.56         8.61        59.41        52.34 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       22.68        43.73        30.18        10.36        15.16        36.03 

$`AMP PEAK  3(1Q44) WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
       61.02        12.99       112.04       112.57        71.80        31.59 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG 
       90.90        43.43       103.10       168.00        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       42.08        12.10        59.57        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        55.73        56.35       145.12        22.62        26.89 
TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS 
      178.32        30.84        79.59        15.19       161.00       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW 
      151.53        54.67        18.12        11.11        48.89        36.03 
TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q 
      176.55        53.92        23.44        28.60        15.68        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 
       17.85        68.25         6.35        29.82         8.65        26.89 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N 
      151.27        91.56        63.35        47.84        64.64        18.61 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 
       37.35        55.92        25.87        17.92        46.82        39.29 
TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       67.43        54.74        79.66        13.91        14.30        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67       129.27        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A3AA 
      103.20        16.96       204.66       158.63       167.90       124.31 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51        13.81       127.20        36.95        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       148.08        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       77.75        98.40        13.02         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       44.05        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
       20.15        31.27        15.16         7.00        38.27        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       94.39       216.92       228.59        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZR 
       48.85        53.52        40.27         9.70       101.26        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
      148.80        49.48        50.14        66.67       174.84        12.43 
TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       26.73        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-AA1V 
       62.79        21.37       294.77         0.33       212.22        42.08 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-YG-AA3P 
       54.38        90.28        56.98         3.75         2.20        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  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 
                     369.93                      294.77 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                     53.225                      47.280 
[1] "0.2 - 369.9 (53.2)" "0.2 - 294.8 (47.3)"
[1] "hr=" "1.2"
D3V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  3(1Q44) MUTATED                   40             4
  AMP PEAK  3(1Q44) WILD-TYPE                 21             1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  3(1Q44) MUTATED                                          40
  AMP PEAK  3(1Q44) WILD-TYPE                                        32
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  3(1Q44) MUTATED                   106
  AMP PEAK  3(1Q44) WILD-TYPE                 103
D3V4, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q44) MUTATED
  DISTANT METASTASIS                                               40
  PRIMARY TUMOR                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        40
  REGIONAL LYMPH NODE                                             106
                                           clus
vv                                          AMP PEAK  3(1Q44) WILD-TYPE
  DISTANT METASTASIS                                                 21
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          32
  REGIONAL LYMPH NODE                                               103
[1] 4 2
[1] 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             5       3      14       10       17
  AMP PEAK  3(1Q44) WILD-TYPE           7       4      14        7       10
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  3(1Q44) MUTATED         16         6         8         7        19
  AMP PEAK  3(1Q44) WILD-TYPE        6         8        11         5        16
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  3(1Q44) MUTATED           11         18         31       11
  AMP PEAK  3(1Q44) WILD-TYPE          4         14         27        8
D3V5, multiclass
             clus
vv            AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  I OR II NOS                         5                           7
  STAGE 0                             3                           4
  STAGE I                            14                          14
  STAGE IA                           10                           7
  STAGE IB                           17                          10
  STAGE II                           16                           6
  STAGE IIA                           6                           8
  STAGE IIB                           8                          11
  STAGE IIC                           7                           5
  STAGE III                          19                          16
  STAGE IIIA                         11                           4
  STAGE IIIB                         18                          14
  STAGE IIIC                         31                          27
  STAGE IV                           11                           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  3(1Q44) MUTATED      36 40 43 36
  AMP PEAK  3(1Q44) WILD-TYPE    27 31 31 31
D3V6, multiclass
       clus
vv      AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  T0+T1                        36                          27
  T2                           40                          31
  T3                           43                          31
  T4                           36                          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  3(1Q44) MUTATED   94 31 23 26
  AMP PEAK  3(1Q44) WILD-TYPE 74 30 15 21
D3V7, multiclass
    clus
vv   AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  N0                        94                          74
  N1                        31                          30
  N2                        23                          15
  N3                        26                          21
[1] 4 2
[1] 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   170   2   2   1   6
  AMP PEAK  3(1Q44) WILD-TYPE 136   2   1   3   3
D3V8, multiclass
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  M0                        170                         136
  M1                          2                           2
  M1A                         2                           1
  M1B                         1                           3
  M1C                         6                           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"
D3V9, binary
                             cls
clus                           0  1
  AMP PEAK  3(1Q44) MUTATED   74 46
  AMP PEAK  3(1Q44) WILD-TYPE 55 41
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     74   46
  AMP PEAK  3(1Q44) WILD-TYPE   55   41
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         74                          55
  YES                        46                          41
[1] 2 2
[1] FALSE
D3V10, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    23 167
  AMP PEAK  3(1Q44) WILD-TYPE  20 137
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     23  167
  AMP PEAK  3(1Q44) WILD-TYPE   20  137
     clus
vv    AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  NO                         23                          20
  YES                       167                         137
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, binary
                             cls
clus                            0   1
  AMP PEAK  3(1Q44) MUTATED    74 117
  AMP PEAK  3(1Q44) WILD-TYPE  57 100
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     74  117
  AMP PEAK  3(1Q44) WILD-TYPE   57  100
        clus
vv       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  FEMALE                        74                          57
  MALE                         117                         100
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q44) MUTATED       3                         0   177
  AMP PEAK  3(1Q44) WILD-TYPE     2                         1   149
D3V13, multiclass
                           clus
vv                          AMP PEAK  3(1Q44) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                           177
                           clus
vv                          AMP PEAK  3(1Q44) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             149
[1] 3 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     5 182
  AMP PEAK  3(1Q44) WILD-TYPE   2 152
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED      5  182
  AMP PEAK  3(1Q44) WILD-TYPE    2  152
                        clus
vv                       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             5                           2
  NOT HISPANIC OR LATINO                       182                         152
[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    60  36
  AMP PEAK  4(3P13) WILD-TYPE 108 129
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         96                         237 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         36                         129 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       44.19         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        29.23        93.21       110.24        52.01        13.68 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
       10.22         4.18        75.65       124.47        11.44         5.56 
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-A5UL 
       17.56        14.83        13.15        23.15        19.00        13.35 
TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H 
        0.20         8.12         5.13        60.23        15.85        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH 
        1.08        39.62         8.84        30.44        32.15        47.21 
TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MP 
       30.08        33.83         5.42         8.84        98.27        26.99 
TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
        5.56        30.15        21.60        22.22        21.73        33.60 
TCGA-ER-A197 TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S 
       12.95       114.15        34.88        13.45        28.60        36.07 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 
       12.62         6.58        22.49         1.71        85.74         6.71 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A4F2 
       13.28         4.70        23.80         7.30        12.89         3.22 
TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        2.27         7.23        31.33        84.72        10.13        15.42 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 
       14.50        15.81         2.99       185.16        11.84         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-Z2-AA3S 
        6.48         7.10        21.83         5.36         1.94         6.67 

$`AMP PEAK  4(3P13) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
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-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       85.32        21.14        68.22        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        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H 
       24.00         6.31         9.34        26.37        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO 
       54.31        32.28        21.44        32.61        25.78        47.87 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ 
       17.72        23.11        29.72        22.06        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      108.79        38.93        87.62        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        5.72        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        62.79         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        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       63.42       125.65       111.91        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       60.49        53.16        52.67       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 
       21.60        16.14         0.95        27.35        18.41        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       18.61        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P 
        3.52        11.90        11.11         4.21        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A3YN 
        1.51        13.08        11.74         9.04         5.62        18.41 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW 
       15.72         3.58         5.36         2.20         3.29        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
        3.45        11.01        14.24        15.52         7.33         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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16        17.33         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.85        11.61        44.28        16.24        12.16        14.70 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       11.84        10.65        14.50        14.50         0.43        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        5.79        18.05         0.33         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       60.03        10.98        71.01        18.67        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
        3.72         3.42         1.08        19.96        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
        4.70         8.22         5.98 

  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                       0.20                        0.13 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                     185.16                      164.19 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                     15.615                      14.560 
[1] "0.2 - 185.2 (15.6)" "0.1 - 164.2 (14.6)"
[1] "hr=" "1.6"
D4V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  4(3P13) MUTATED    60  36
  AMP PEAK  4(3P13) WILD-TYPE 113 130
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         96                         243 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         36                         130 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       62.07       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        45.30       174.84       125.79       135.75       178.32 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
       11.61        58.52        95.24       161.00        29.06       129.63 
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        68.25        54.02        17.29 
TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H 
       12.20        94.98        68.15       133.81        91.56        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GH 
        2.60        56.84        14.47       369.93       195.02       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       109.58       148.08 
TCGA-ER-A197 TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S 
       13.94       268.93       152.35       131.51        61.05        37.25 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 
       31.27        80.32        46.98        33.21       174.21       210.08 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A4F2 
       38.27        29.46       202.65        27.72        23.93        50.14 
TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       77.88         7.23       117.93        84.72        10.13        62.79 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 
       21.37        65.88         4.01       219.16        24.03        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-Z2-AA3S 
       54.38         8.61        22.68        43.73        10.36        93.07 

$`AMP PEAK  4(3P13) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
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-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
      103.10        23.77       168.00        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        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H 
       24.53        13.87         9.34        39.75        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO 
      145.12        32.94        22.62        63.81        26.89       137.92 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        79.59        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      170.20        89.13       137.79       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         6.41        18.12        11.34        22.29        11.11 
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-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      176.55        61.18        53.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       10.49        10.16        17.85        52.01         6.35        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         4.96 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.97        63.78        72.07        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        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR 
       89.33        54.74        79.66        75.48       126.81        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       55.59        44.88        94.82        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       203.05       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40       162.48        71.21       124.31       122.73        51.62 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 
       64.08        34.32       201.80        27.35        51.35        31.40 
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-A19E TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P 
       12.59        13.02        26.37         6.44        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A3YN 
       20.15        16.37        32.05       247.04         6.77        92.98 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW 
       15.72        15.16         7.00        34.82        94.39       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
       48.59       228.59        20.91        28.08         7.79        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-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38       101.26        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-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
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        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        2.04        11.74       139.89        64.44        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       46.36        12.62        50.10        59.41       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        6.67        18.05         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      121.08        42.08       105.04        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       52.34         3.75         2.20        30.18        15.16        36.03 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
       14.43        23.64        11.74 

  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 
                     369.93                      357.37 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                      62.43                       47.38 
[1] "2.6 - 369.9 (62.4)" "0.2 - 357.4 (47.4)"
[1] "hr=" "1.8"
D4V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  4(3P13) MUTATED                   17             2
  AMP PEAK  4(3P13) WILD-TYPE                 44             3
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  4(3P13) MUTATED                                          19
  AMP PEAK  4(3P13) WILD-TYPE                                        53
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  4(3P13) MUTATED                    60
  AMP PEAK  4(3P13) WILD-TYPE                 149
D4V4, multiclass
                                           clus
vv                                          AMP PEAK  4(3P13) MUTATED
  DISTANT METASTASIS                                               17
  PRIMARY TUMOR                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        19
  REGIONAL LYMPH NODE                                              60
                                           clus
vv                                          AMP PEAK  4(3P13) WILD-TYPE
  DISTANT METASTASIS                                                 44
  PRIMARY TUMOR                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          53
  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  4(3P13) MUTATED             6       2       8        8        9
  AMP PEAK  4(3P13) WILD-TYPE           6       5      20        9       18
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  4(3P13) MUTATED          5         2         2         4        10
  AMP PEAK  4(3P13) WILD-TYPE       17        12        17         8        25
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  4(3P13) MUTATED            5         12         13        3
  AMP PEAK  4(3P13) WILD-TYPE         10         20         45       16
D4V5, multiclass
             clus
vv            AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  I OR II NOS                         6                           6
  STAGE 0                             2                           5
  STAGE I                             8                          20
  STAGE IA                            8                           9
  STAGE IB                            9                          18
  STAGE II                            5                          17
  STAGE IIA                           2                          12
  STAGE IIB                           2                          17
  STAGE IIC                           4                           8
  STAGE III                          10                          25
  STAGE IIIA                          5                          10
  STAGE IIIB                         12                          20
  STAGE IIIC                         13                          45
  STAGE IV                            3                          16
[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      20 23 16 19
  AMP PEAK  4(3P13) WILD-TYPE    43 48 58 48
D4V6, multiclass
       clus
vv      AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  T0+T1                        20                          43
  T2                           23                          48
  T3                           16                          58
  T4                           19                          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  4(3P13) MUTATED    51  19   9  10
  AMP PEAK  4(3P13) WILD-TYPE 117  42  29  37
D4V7, multiclass
    clus
vv   AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  N0                        51                         117
  N1                        19                          42
  N2                         9                          29
  N3                        10                          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                           M0  M1 M1A M1B M1C
  AMP PEAK  4(3P13) MUTATED    89   0   1   0   2
  AMP PEAK  4(3P13) WILD-TYPE 217   4   2   4   7
D4V8, multiclass
     clus
vv    AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  M0                         89                         217
  M1                          0                           4
  M1A                         1                           2
  M1B                         0                           4
  M1C                         2                           7
[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   38 25
  AMP PEAK  4(3P13) WILD-TYPE 91 62
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     38   25
  AMP PEAK  4(3P13) WILD-TYPE   91   62
     clus
vv    AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  NO                         38                          91
  YES                        25                          62
[1] 2 2
[1] FALSE
D4V10, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED    10  89
  AMP PEAK  4(3P13) WILD-TYPE  33 215
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     10   89
  AMP PEAK  4(3P13) WILD-TYPE   33  215
     clus
vv    AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  NO                         10                          33
  YES                        89                         215
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, binary
                             cls
clus                            0   1
  AMP PEAK  4(3P13) MUTATED    46  53
  AMP PEAK  4(3P13) WILD-TYPE  85 164
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     46   53
  AMP PEAK  4(3P13) WILD-TYPE   85  164
        clus
vv       AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  FEMALE                        46                          85
  MALE                          53                         164
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3P13) MUTATED       2                         0    91
  AMP PEAK  4(3P13) WILD-TYPE     3                         1   235
D4V13, multiclass
                           clus
vv                          AMP PEAK  4(3P13) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            91
                           clus
vv                          AMP PEAK  4(3P13) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             235
[1] 3 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  96
  AMP PEAK  4(3P13) WILD-TYPE   7 238
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED      0   96
  AMP PEAK  4(3P13) WILD-TYPE    7  238
                        clus
vv                       AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  HISPANIC OR LATINO                             0                           7
  NOT HISPANIC OR LATINO                        96                         238
[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    27  34
  AMP PEAK  5(4Q12) WILD-TYPE 141 131
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         61                         272 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         34                         131 
$`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        32.28 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6EA 
       23.11        29.72        87.62        24.07        21.93        11.31 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH 
       48.79        35.80        39.19        22.36        17.56         0.13 
TCGA-EB-A5SH TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G 
       19.00         1.12         5.13        15.85        11.15         8.55 
TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP 
       12.03        51.12        30.08         5.42        63.42        26.99 
TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       60.49       124.31         3.68         3.22        21.60        22.22 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A2ND TCGA-ER-A3ET 
        0.95        33.60        12.95        25.18         1.87         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZJ 
       22.49         1.71        18.41         2.20         3.45        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GF-A4EO 
       12.89        47.38         8.65         8.68        28.73         7.23 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A9SD TCGA-W3-AA1V 
       31.33        15.42        14.70        14.50        14.50        10.98 
TCGA-WE-A8ZQ 
        3.72 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97        16.47       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        44.19         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        64.44        59.57       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        24.00         6.31         9.34       103.59 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       29.23        93.21        54.74        31.30        54.31        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.61        25.78       110.24        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       17.72        22.06        10.22        15.19         4.18       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      108.79        38.93        75.65       124.47        11.44         5.56 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
        4.01         5.72         9.90        13.22        14.60        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
        4.93         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.20        23.15        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       10.55         6.31         8.12         1.35        12.20         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       60.23         4.34         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        62.79        36.85         1.08        39.62         9.50 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        8.09         8.84         9.99        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       14.56       125.65       111.91        56.02        25.08        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       53.16        52.67         5.56       122.73        51.62        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-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        18.41        21.73        31.40        18.61        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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
        5.62        85.74        15.72         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       13.28         4.70         3.29        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-A1ZH TCGA-FS-A1ZP 
        8.22        19.53        11.08         7.17        30.87        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15        40.64        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         3.22         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 
       17.33         9.90         0.85        11.61        44.28        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
       10.13        16.24        12.16        11.84        10.65        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       15.81         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       164.19         8.98        60.03         2.99       185.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       71.01        11.84         5.49         6.48         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       21.07        13.12         3.42        21.83         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       19.96         1.94        12.07         6.18         4.70         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       0.13                        0.13 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     124.31                      185.16 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      15.42                       14.53 
[1] "0.1 - 124.3 (15.4)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.3"
D5V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    27  34
  AMP PEAK  5(4Q12) WILD-TYPE 146 132
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         61                         278 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         34                         132 
$`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        32.94 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6EA 
      125.19        30.84       137.79       117.17        22.29        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH 
       48.89        36.03       194.83        23.44       215.44        17.85 
TCGA-EB-A5SH TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G 
       54.02        33.73        68.15        91.56        13.97        72.07 
TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP 
       56.42        59.28        48.72        13.91        96.23       248.65 
TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
      134.40       124.31         3.68       172.18        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A2ND TCGA-ER-A3ET 
      201.80       148.08        13.94        98.40        23.34        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZJ 
       46.98        33.21        92.98        34.82        48.59        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GF-A4EO 
       23.93       101.26       133.55        26.56        28.73         7.23 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A9SD TCGA-W3-AA1V 
      117.93        62.79        39.58        50.10        59.41        42.08 
TCGA-WE-A8ZQ 
       52.34 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        66.08        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       45.30       174.84        55.73        56.35       145.12        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       18.18        79.59        11.61        15.19        58.52       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13        95.24       161.00        29.06       129.63 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
       11.11         9.90        66.25        22.95       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-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-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        94.98        14.70        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      133.81       151.27       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       47.84        63.78        64.64         2.60        56.84        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       37.35        14.47        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       161.03       208.04        89.33        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       126.81        14.30        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
      204.66       158.63       203.05       167.90        47.54        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      162.48        71.21        53.26       122.73        51.62        54.51 
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-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       109.58        31.40        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
        6.77       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27        29.46        94.39       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-A1ZP 
       53.52        40.27        15.45         9.70        32.75        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-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-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 
       19.30         9.90         2.04        11.74       139.89        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
       10.13        64.44        32.48        46.36        12.62        21.37 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       212.22        63.02       121.08         4.01       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      105.04        24.03        38.56        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       56.98        59.41         3.75        22.68        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       30.18        10.36        15.16        36.03        14.43        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       3.68                        0.16 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     248.65                      369.93 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      52.34                       49.81 
[1] "3.7 - 248.7 (52.3)" "0.2 - 369.9 (49.8)"
[1] "hr=" "1.2"
D5V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  5(4Q12) MUTATED                   11             1
  AMP PEAK  5(4Q12) WILD-TYPE                 50             4
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  5(4Q12) MUTATED                                          12
  AMP PEAK  5(4Q12) WILD-TYPE                                        60
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  5(4Q12) MUTATED                    38
  AMP PEAK  5(4Q12) WILD-TYPE                 171
D5V4, multiclass
                                           clus
vv                                          AMP PEAK  5(4Q12) MUTATED
  DISTANT METASTASIS                                               11
  PRIMARY TUMOR                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        12
  REGIONAL LYMPH NODE                                              38
                                           clus
vv                                          AMP PEAK  5(4Q12) WILD-TYPE
  DISTANT METASTASIS                                                 50
  PRIMARY TUMOR                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          60
  REGIONAL LYMPH NODE                                               171
[1] 4 2
[1] 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             2       0       8        2        8
  AMP PEAK  5(4Q12) WILD-TYPE          10       7      20       15       19
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  5(4Q12) MUTATED          3         1         2         4        10
  AMP PEAK  5(4Q12) WILD-TYPE       19        13        17         8        25
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  5(4Q12) MUTATED            3          8          7        2
  AMP PEAK  5(4Q12) WILD-TYPE         12         24         51       17
D5V5, multiclass
             clus
vv            AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  I OR II NOS                         2                          10
  STAGE 0                             0                           7
  STAGE I                             8                          20
  STAGE IA                            2                          15
  STAGE IB                            8                          19
  STAGE II                            3                          19
  STAGE IIA                           1                          13
  STAGE IIB                           2                          17
  STAGE IIC                           4                           8
  STAGE III                          10                          25
  STAGE IIIA                          3                          12
  STAGE IIIB                          8                          24
  STAGE IIIC                          7                          51
  STAGE IV                            2                          17
[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      17 17 11 13
  AMP PEAK  5(4Q12) WILD-TYPE    46 54 63 54
D5V6, multiclass
       clus
vv      AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  T0+T1                        17                          46
  T2                           17                          54
  T3                           11                          63
  T4                           13                          54
[1] 4 2
[1] 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    33  12   8   6
  AMP PEAK  5(4Q12) WILD-TYPE 135  49  30  41
D5V7, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  N0                        33                         135
  N1                        12                          49
  N2                         8                          30
  N3                         6                          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                           M0  M1 M1A M1B M1C
  AMP PEAK  5(4Q12) MUTATED    57   0   1   1   0
  AMP PEAK  5(4Q12) WILD-TYPE 249   4   2   3   9
D5V8, multiclass
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  M0                         57                         249
  M1                          0                           4
  M1A                         1                           2
  M1B                         1                           3
  M1C                         0                           9
[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    26  13
  AMP PEAK  5(4Q12) WILD-TYPE 103  74
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     26   13
  AMP PEAK  5(4Q12) WILD-TYPE  103   74
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                         26                         103
  YES                        13                          74
[1] 2 2
[1] FALSE
D5V10, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     7  56
  AMP PEAK  5(4Q12) WILD-TYPE  36 248
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      7   56
  AMP PEAK  5(4Q12) WILD-TYPE   36  248
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          7                          36
  YES                        56                         248
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    24  39
  AMP PEAK  5(4Q12) WILD-TYPE 107 178
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     24   39
  AMP PEAK  5(4Q12) WILD-TYPE  107  178
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        24                         107
  MALE                          39                         178
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED       1                         0    61
  AMP PEAK  5(4Q12) WILD-TYPE     4                         1   265
D5V13, multiclass
                           clus
vv                          AMP PEAK  5(4Q12) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            61
                           clus
vv                          AMP PEAK  5(4Q12) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             265
[1] 3 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     2  61
  AMP PEAK  5(4Q12) WILD-TYPE   5 273
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      2   61
  AMP PEAK  5(4Q12) WILD-TYPE    5  273
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             2                           5
  NOT HISPANIC OR LATINO                        61                         273
[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    51  49
  AMP PEAK  6(5P15.33) WILD-TYPE 117 116
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           100                            233 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            49                            116 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK 
        3.02         8.52        22.55        86.76        44.19         6.31 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
       56.19        64.44        59.57        15.25        61.38        24.00 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO 
       26.37        93.21        32.28        21.44        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A6E9 
       13.68        17.72        23.11         4.18        75.65         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       11.31        13.22        48.79        13.68         7.00        17.56 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 
       13.15         0.20         0.13         8.12         1.12         5.13 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       60.23         9.21         1.18        11.15        62.79         8.55 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2M6 
       39.62        30.44        32.15        11.31        28.31        98.27 
TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
        2.70        26.99        53.16       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI 
       30.15        15.95        12.72         3.22        22.22        33.60 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N 
       12.95        25.18         3.78       114.15        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH 
       34.68         9.57         6.58         1.87        13.08        11.74 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YX 
        1.71        85.74         5.36         2.20         4.70         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 TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ 
       10.65        18.05         2.99        10.98       185.16        11.84 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-YG-AA3P TCGA-Z2-A8RT 
       18.67         3.72         4.70         8.22 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        6.97         6.97        16.47       111.09        32.42        70.16 
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-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
        8.38        21.14        88.50        68.22        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       36.16        92.42       114.67        46.98        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F 
       13.32         6.31         9.34       103.59        29.23        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GB 
       31.30        54.31        32.61        25.78       110.24        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       22.06        10.22        15.19       142.45       108.79        38.93 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      124.47        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       21.93         5.72        14.60        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5SH 
       22.36         6.64        19.36        14.83        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A 
        1.35        12.20         4.31         4.34        15.85         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        9.90        37.97        36.85         1.08         9.50        12.03 
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-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        55.69         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       36.33         8.84         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49        52.67 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
        5.56        51.62        13.81        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       16.14         0.95        27.35        18.41        21.73        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       22.49         5.62        18.41        15.72         6.71         3.58 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       13.28         3.29        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-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
       11.08        30.87        12.92        47.38        52.08         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-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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
        0.20         0.99         0.16        17.33         9.90         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       11.61        44.28        10.13        16.24        15.42        12.16 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       11.84        14.50        14.50        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       11.05         5.79         0.33         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
       60.03        71.01         5.49         6.48         7.10        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       13.12         3.42        21.83         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         6.18         6.67         5.98 

  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                          0.13                           0.16 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                        185.16                         164.19 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                         13.68                          15.19 
[1] "0.1 - 185.2 (13.7)" "0.2 - 164.2 (15.2)"
[1] "hr=" "1"  
D6V2, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(5P15.33) MUTATED    54  49
  AMP PEAK  6(5P15.33) WILD-TYPE 119 117
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           103                            236 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            49                            117 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK 
       17.03        16.67        31.59        86.76        62.07        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
       56.19        66.08        59.57        58.06        86.93        24.53 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO 
       39.75       174.84        32.94        22.62       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A148 
      178.32        18.18       125.19        58.52        95.24       151.53 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        3.65        18.12         9.90        25.18        66.25        48.89 
TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
      176.55        10.49       215.44        13.87        10.16        17.85 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I 
       94.98        33.73        68.15       133.81       168.26        13.55 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W 
       13.97        63.78        72.07        56.84       369.93       195.02 
TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS 
       46.82        75.48       129.27        28.83       248.65       162.48 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      124.31       122.73         3.68        54.51        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C 
      172.18        53.19       148.08        13.94        98.40        48.89 
TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T 
      268.93        61.05        44.05       162.08        50.89         8.88 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U9 
       23.34        16.37        32.05        33.21       174.21         7.00 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK 
       34.82        29.46        48.59        40.27         9.70        23.93 
TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FW-A3TU TCGA-GF-A4EO 
      133.55        27.09        66.67        28.73        47.54         7.23 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-QB-AA9O TCGA-W3-AA1O 
      117.93        84.72        39.58        12.62        18.05         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-YG-AA3P 
       42.08       219.16        24.03        90.28        52.34        14.43 
TCGA-Z2-A8RT 
       23.64 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       61.02        12.99        16.57       112.04       112.57        71.80 
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-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG 
       65.49        23.77       115.53       168.00        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       42.08       171.58       130.72        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F 
       60.23        13.87         9.34       103.59        45.30        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A8GB 
       56.35       145.12        63.81        26.89       125.79        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        11.61        15.19       228.99       170.20        89.13 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 
      161.00       137.79        29.06       129.63       117.17        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HW 
        6.41        11.34        22.29        11.11        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       194.83        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
       53.92        65.92        23.44        68.09        28.60        15.68 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       29.82        27.22         8.65        14.70        26.89         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H 
      151.27        91.56        63.35        80.61        47.84        64.64 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        2.60        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       25.87        17.92       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       89.33        54.74        79.66        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
       14.30        55.59        44.88        94.82        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF 
       43.23       134.40        71.21        53.26        51.62        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       51.35       109.58        31.40        35.44        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-A19L TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      131.51        37.25       148.18        79.99        43.82        20.15 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       31.27       247.04        80.32        46.98         6.77        92.98 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW 
       15.72       210.08        15.16        38.27        94.39       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-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85       357.37        53.52        15.45        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        74.73        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        27.02        77.82        50.14       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 
       19.30         9.90         2.04        11.74       139.89        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       64.44        62.79        32.48        46.36        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       59.41        65.88       357.04       294.77         6.67         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-A8K1 
        0.69       212.22        63.02       121.08       105.04        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
       54.38         8.61        56.98        59.41         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        15.16        36.03 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  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 
                        369.93                         357.37 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                         48.89                          50.45 
[1] "3.6 - 369.9 (48.9)" "0.2 - 357.4 (50.5)"
[1] "hr=" "1.1"
D6V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  6(5P15.33) MUTATED                   16             5
  AMP PEAK  6(5P15.33) WILD-TYPE                 45             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  6(5P15.33) MUTATED                                          18
  AMP PEAK  6(5P15.33) WILD-TYPE                                        54
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  6(5P15.33) MUTATED                    66
  AMP PEAK  6(5P15.33) WILD-TYPE                 143
D6V4, multiclass
                                           clus
vv                                          AMP PEAK  6(5P15.33) MUTATED
  DISTANT METASTASIS                                                  16
  PRIMARY TUMOR                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           18
  REGIONAL LYMPH NODE                                                 66
                                           clus
vv                                          AMP PEAK  6(5P15.33) WILD-TYPE
  DISTANT METASTASIS                                                    45
  PRIMARY TUMOR                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             54
  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  6(5P15.33) MUTATED             3       2       7        4        8
  AMP PEAK  6(5P15.33) WILD-TYPE           9       5      21       13       19
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  6(5P15.33) MUTATED         10         3         5         6
  AMP PEAK  6(5P15.33) WILD-TYPE       12        11        14         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  6(5P15.33) MUTATED          10          4         10         17
  AMP PEAK  6(5P15.33) WILD-TYPE        25         11         22         41
                                vv
clus                             STAGE IV
  AMP PEAK  6(5P15.33) MUTATED          5
  AMP PEAK  6(5P15.33) WILD-TYPE       14
D6V5, multiclass
             clus
vv            AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  I OR II NOS                            3                              9
  STAGE 0                                2                              5
  STAGE I                                7                             21
  STAGE IA                               4                             13
  STAGE IB                               8                             19
  STAGE II                              10                             12
  STAGE IIA                              3                             11
  STAGE IIB                              5                             14
  STAGE IIC                              6                              6
  STAGE III                             10                             25
  STAGE IIIA                             4                             11
  STAGE IIIB                            10                             22
  STAGE IIIC                            17                             41
  STAGE IV                               5                             14
[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      24 16 22 23
  AMP PEAK  6(5P15.33) WILD-TYPE    39 55 52 44
D6V6, multiclass
       clus
vv      AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  T0+T1                           24                             39
  T2                              16                             55
  T3                              22                             52
  T4                              23                             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  6(5P15.33) MUTATED    53  13  17  16
  AMP PEAK  6(5P15.33) WILD-TYPE 115  48  21  31
D6V7, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  N0                           53                            115
  N1                           13                             48
  N2                           17                             21
  N3                           16                             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  6(5P15.33) MUTATED    94   0   2   1   3
  AMP PEAK  6(5P15.33) WILD-TYPE 212   4   1   3   6
D6V8, multiclass
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  M0                            94                            212
  M1                             0                              4
  M1A                            2                              1
  M1B                            1                              3
  M1C                            3                              6
[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   39 27
  AMP PEAK  6(5P15.33) WILD-TYPE 90 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     39   27
  AMP PEAK  6(5P15.33) WILD-TYPE   90   60
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                            39                             90
  YES                           27                             60
[1] 2 2
[1] FALSE
D6V10, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    15  91
  AMP PEAK  6(5P15.33) WILD-TYPE  28 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     15   91
  AMP PEAK  6(5P15.33) WILD-TYPE   28  213
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                            15                             28
  YES                           91                            213
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    39  67
  AMP PEAK  6(5P15.33) WILD-TYPE  92 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     39   67
  AMP PEAK  6(5P15.33) WILD-TYPE   92  150
        clus
vv       AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  FEMALE                           39                             92
  MALE                             67                            150
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(5P15.33) MUTATED       3                         0    99
  AMP PEAK  6(5P15.33) WILD-TYPE     2                         1   227
D6V13, multiclass
                           clus
vv                          AMP PEAK  6(5P15.33) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               99
                           clus
vv                          AMP PEAK  6(5P15.33) WILD-TYPE
  ASIAN                                                  2
  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"
D6V14, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED     3 101
  AMP PEAK  6(5P15.33) WILD-TYPE   4 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      3  101
  AMP PEAK  6(5P15.33) WILD-TYPE    4  233
                        clus
vv                       AMP PEAK  6(5P15.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          101
                        clus
vv                       AMP PEAK  6(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            233
[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    27  26
  AMP PEAK  7(5Q35.3) WILD-TYPE 141 139
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           53                           280 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           26                           139 
$`AMP PEAK  7(5Q35.3) MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CF 
        3.02         8.52        44.19        56.19        59.57        24.00 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       26.37        32.28        21.44        13.68        23.11        22.06 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EB-A44Q TCGA-EE-A180 TCGA-EE-A182 
        9.90        11.31         4.93        13.15         8.12         1.35 
TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GJ 
        9.21        36.85         8.84        30.44        32.15        19.43 
TCGA-EE-A2M7 TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3JA 
        2.70        53.16        52.67       124.31         3.22        22.22 
TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2ND 
       33.60         3.78        11.11        34.68         6.58         1.87 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YX 
        6.58         1.71         5.36         2.20         4.70         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 TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3P 
        0.85        10.65        11.84         3.72         4.70 

$`AMP PEAK  7(5Q35.3) WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        6.97         6.97        16.47       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.79        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       11.41         7.50        36.16         6.31        92.42        64.44 
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-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E 
       13.32         6.31         9.34       103.59        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.74        31.30        54.31        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
       52.01        47.87        17.72        29.72        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
        4.18       142.45       108.79        38.93        75.65       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        5.72        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-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       14.83         0.20         0.13        23.15        19.00        13.35 
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-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        60.23         4.34        15.85 
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        62.79 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55         1.08        39.62         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        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        30.08        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 
       55.69         5.42         1.15        13.02        34.98        36.33 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        60.49 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72        22.92        21.60        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
        0.95        27.35        18.41        21.73        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       12.95        38.40         5.72        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
        1.51        13.08        12.62        11.74         9.04        22.49 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       13.28         3.29        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-A1ZE 
       15.52         7.33         7.30         3.39        20.38        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       11.08         7.17        30.87        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-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-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
        5.98         6.41         2.27         0.99         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        11.61        44.28        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       10.13        16.24        15.42        12.16        14.70        11.84 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       14.50        14.50        14.50        15.81         0.43        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        5.79        18.05         0.33         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       60.03         2.99        10.98       185.16        71.01         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
        6.48         7.10        18.67        21.07        13.12         3.42 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       21.83         5.36         1.08        19.96         1.94        12.07 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         8.22         6.67         5.98 

  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                         0.13                          0.13 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                       124.31                        185.16 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                       11.110                        15.765 
[1] "0.1 - 124.3 (11.1)" "0.1 - 185.2 (15.8)"
[1] "hr=" "1.3"
D7V2, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(5Q35.3) MUTATED    29  26
  AMP PEAK  7(5Q35.3) WILD-TYPE 144 140
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           55                           284 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           26                           140 
$`AMP PEAK  7(5Q35.3) MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CF 
       17.03        16.67        62.07        56.19        59.57        24.53 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       39.75        32.94        22.62       178.32       125.19        79.59 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EB-A44Q 
      151.53         3.65         9.90        25.18        65.92        13.87 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A29T 
       94.98        14.70       168.26        64.64        14.47       369.93 
TCGA-EE-A29W TCGA-EE-A2GJ TCGA-EE-A2M7 TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      195.02        89.33        28.83       162.48        71.21       124.31 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19P 
      172.18        53.19       148.08        48.89        26.37       162.08 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7U9 TCGA-FR-A8YC 
        8.88        23.34        80.32        33.21         7.00        34.82 
TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A4F5 
       29.46        48.59        53.52        47.38        23.93        28.73 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A4U9 TCGA-WE-A8JZ TCGA-WE-A8ZQ 
        0.20        47.54         2.04        12.62        24.03        52.34 
TCGA-YG-AA3P 
       14.43 

$`AMP PEAK  7(5Q35.3) WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       61.02        12.99        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       11.87       113.52        42.08        12.10       171.58        66.08 
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-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        13.87         9.34       103.59        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       55.73        56.35       145.12        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
      135.75       137.92        18.18        30.84        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       58.52       228.99       170.20        89.13        95.24       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX 
      137.79        29.06       129.63       117.17        54.67         6.41 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       18.12        11.34        22.29        11.11        66.25        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-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-A44R TCGA-EB-A5KH 
       28.60        10.49       215.44        15.68        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       29.82        27.22         8.65        33.73        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.96       133.81       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       80.61        47.84        13.97        63.78        72.07         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       56.84        18.61        56.42        37.35        55.92        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       208.04        48.72 
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       126.81        13.91 
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-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB 
       47.54       248.65        43.23       134.40        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       109.58        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
        9.17        77.75        98.40        12.59        13.02       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       31.27        32.05       247.04        46.98         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YE 
      174.21        15.72       210.08        15.16        38.27        94.39 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92       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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75       101.26        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-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       77.88        22.92         0.16        19.30         9.90         7.23 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       62.79        32.48        39.58        46.36        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16       105.04        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       90.28        56.98        59.41         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT 
        2.20        30.18        10.36        15.16        36.03        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  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 
                       369.93                        357.37 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                       47.380                        51.485 
[1] "0.2 - 369.9 (47.4)" "0.2 - 357.4 (51.5)"
[1] "hr=" "1.1"
D7V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  7(5Q35.3) MUTATED                   13             3
  AMP PEAK  7(5Q35.3) WILD-TYPE                 48             2
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  7(5Q35.3) MUTATED                                           5
  AMP PEAK  7(5Q35.3) WILD-TYPE                                        67
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK  7(5Q35.3) MUTATED                    36
  AMP PEAK  7(5Q35.3) WILD-TYPE                 173
D7V4, multiclass
                                           clus
vv                                          AMP PEAK  7(5Q35.3) MUTATED
  DISTANT METASTASIS                                                 13
  PRIMARY TUMOR                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           5
  REGIONAL LYMPH NODE                                                36
                                           clus
vv                                          AMP PEAK  7(5Q35.3) WILD-TYPE
  DISTANT METASTASIS                                                   48
  PRIMARY TUMOR                                                         2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            67
  REGIONAL LYMPH NODE                                                 173
[1] 4 2
[1] 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             2       1       5        4        5
  AMP PEAK  7(5Q35.3) WILD-TYPE          10       6      23       13       22
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  7(5Q35.3) MUTATED          3         2         3         2
  AMP PEAK  7(5Q35.3) WILD-TYPE       19        12        16        10
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  7(5Q35.3) MUTATED           4          3          3         10
  AMP PEAK  7(5Q35.3) WILD-TYPE        31         12         29         48
                               vv
clus                            STAGE IV
  AMP PEAK  7(5Q35.3) MUTATED          4
  AMP PEAK  7(5Q35.3) WILD-TYPE       15
D7V5, multiclass
             clus
vv            AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  I OR II NOS                           2                            10
  STAGE 0                               1                             6
  STAGE I                               5                            23
  STAGE IA                              4                            13
  STAGE IB                              5                            22
  STAGE II                              3                            19
  STAGE IIA                             2                            12
  STAGE IIB                             3                            16
  STAGE IIC                             2                            10
  STAGE III                             4                            31
  STAGE IIIA                            3                            12
  STAGE IIIB                            3                            29
  STAGE IIIC                           10                            48
  STAGE IV                              4                            15
[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      12 13 11 11
  AMP PEAK  7(5Q35.3) WILD-TYPE    51 58 63 56
D7V6, multiclass
       clus
vv      AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  T0+T1                          12                            51
  T2                             13                            58
  T3                             11                            63
  T4                             11                            56
[1] 4 2
[1] 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    29   8   4  11
  AMP PEAK  7(5Q35.3) WILD-TYPE 139  53  34  36
D7V7, multiclass
    clus
vv   AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  N0                          29                           139
  N1                           8                            53
  N2                           4                            34
  N3                          11                            36
[1] 4 2
[1] 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    51   1   2   1   1
  AMP PEAK  7(5Q35.3) WILD-TYPE 255   3   1   3   8
D7V8, multiclass
     clus
vv    AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  M0                           51                           255
  M1                            1                             3
  M1A                           2                             1
  M1B                           1                             3
  M1C                           1                             8
[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    24  13
  AMP PEAK  7(5Q35.3) WILD-TYPE 105  74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED     24   13
  AMP PEAK  7(5Q35.3) WILD-TYPE  105   74
     clus
vv    AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  NO                           24                           105
  YES                          13                            74
[1] 2 2
[1] FALSE
D7V10, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED     6  51
  AMP PEAK  7(5Q35.3) WILD-TYPE  37 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED      6   51
  AMP PEAK  7(5Q35.3) WILD-TYPE   37  253
     clus
vv    AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  NO                            6                            37
  YES                          51                           253
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.3) MUTATED    24  33
  AMP PEAK  7(5Q35.3) WILD-TYPE 107 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED     24   33
  AMP PEAK  7(5Q35.3) WILD-TYPE  107  184
        clus
vv       AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  FEMALE                          24                           107
  MALE                            33                           184
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5Q35.3) MUTATED       1                         0    53
  AMP PEAK  7(5Q35.3) WILD-TYPE     4                         1   273
D7V13, multiclass
                           clus
vv                          AMP PEAK  7(5Q35.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              53
                           clus
vv                          AMP PEAK  7(5Q35.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               273
[1] 3 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     3  53
  AMP PEAK  7(5Q35.3) WILD-TYPE   4 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED      3   53
  AMP PEAK  7(5Q35.3) WILD-TYPE    4  281
                        clus
vv                       AMP PEAK  7(5Q35.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       AMP PEAK  7(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           281
[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    84 107
  AMP PEAK  8(6P24.3) WILD-TYPE  84  58
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          191                           142 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          107                            58 
$`AMP PEAK  8(6P24.3) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
        6.97        16.47         8.52       110.79        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG 
       81.24         8.38        21.14        68.22        44.19         7.50 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU 
       64.44        15.25        61.38         6.31       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       29.23        93.21        32.28        25.78        52.01        47.87 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       23.11        10.22       142.45       108.79        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
       87.62        11.44         5.72         9.90        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA 
       48.79        10.03        39.19        13.68         9.99         4.93 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
        6.64         7.00        13.15         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       13.35        10.55         6.31         8.12         1.12        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
        5.13         4.31        60.23         9.21         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       11.15         8.55         1.08        12.03         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH 
        2.43         8.09         9.67        51.12        17.98        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       19.43        35.54        33.83         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2ME 
       34.98        36.33        98.27         2.70         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
        2.73        14.56        63.42       125.65        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD 
       26.99        21.60        53.16         5.56       124.31         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        15.95         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       16.14        22.22         0.95        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       11.80        13.08         9.04         6.58        22.49         1.71 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
       15.72         6.71         3.58         2.20         4.70        64.47 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC 
        3.45        23.80        14.24        15.52         7.30        20.38 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       19.53         7.17        30.87        12.89        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3I3 
        3.22        28.73        14.20        10.78         2.27         0.20 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        0.13         7.23        11.61        31.33        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       15.42        12.16        14.70        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       14.50         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 
        0.69         8.98        10.98        71.01        11.84         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
        7.10        18.67        13.12         3.72         3.42        21.83 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
       19.96         1.94        12.07         6.18         4.70 

$`AMP PEAK  8(6P24.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
        3.02         6.97       111.09        32.42        70.16        28.08 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH 
       10.29        85.32        88.50        86.76        11.41        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
        6.31        92.42        56.19        59.57       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51F 
       46.32        82.29        13.32        24.00         9.34        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR 
       31.30        54.31        21.44        32.61       110.24        13.68 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GM 
       17.72        29.72        22.06        15.19         4.18        75.65 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HW 
        5.56        24.07         4.01        21.93        11.31        35.80 
TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 
       51.12        44.52        36.69        25.15        22.36        19.36 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       17.56        14.83         0.20        13.22         0.20        11.57 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29E 
        1.35         4.34        15.85         1.18        37.97        62.79 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       36.85        39.62         9.50         8.09        30.44        32.15 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE 
       11.31        49.22        36.30        36.33        34.29        60.00 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M8 
       30.08        16.01        28.31        55.69         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT 
       47.51        44.25         7.96       111.91        60.49        52.67 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3JD TCGA-EE-A3JE 
      122.73        51.62        30.15        12.72        27.35        18.41 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       21.73        31.40        18.61        38.40        76.41        25.18 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
      114.15        34.88        13.45        78.44         1.87         1.51 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U9 
       12.62        11.74         5.62        18.41        85.74         5.36 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
       13.28         3.29        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        17.33         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A4U8 TCGA-HR-A2OH TCGA-W3-A824 
        0.85        44.28        84.72        11.84        15.81       164.19 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZY 
       60.03         2.99       185.16         5.49        21.07         5.36 
TCGA-WE-AA9Y TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.08         8.22         6.67         5.98 

  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                         0.13                          0.16 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                       142.45                        185.16 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                       13.080                        21.585 
[1] "0.1 - 142.4 (13.1)" "0.2 - 185.2 (21.6)"
[1] "hr=" "1.8"
D8V2, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(6P24.3) MUTATED    88 107
  AMP PEAK  8(6P24.3) WILD-TYPE  85  59
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          195                           144 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                          107                            59 
$`AMP PEAK  8(6P24.3) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       61.02        16.57        16.67       133.25        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG 
       95.74        65.49        23.77       168.00        62.07       113.52 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU 
       66.08        58.06        86.93        13.87       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       45.30       174.84        32.94        26.89       135.75       137.92 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
      125.19        11.61       228.99       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 
      137.79        29.06       151.53        54.67         3.65        18.12 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I0 
       11.11         9.90        66.25        22.95        48.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 
      194.83       176.55        35.93        65.92        68.09        10.49 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17Y 
       13.87        17.85        68.25        54.02        17.29        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
      133.81       168.26        63.35        80.61        13.97        72.07 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        2.60        56.42        14.47        55.92        25.87        17.92 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GL 
       39.29        59.28       314.56       208.04        89.33        79.66 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI 
      129.27        28.83        47.28       103.27       268.73       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       158.63       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      162.48        53.26       124.31         3.68        13.81        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
      201.80       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-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NF 
       50.89        37.25         8.88       148.18        43.82        16.37 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 
      247.04        80.32        46.98        33.21        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
       15.16        34.82        29.46       216.92        48.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG 
       20.91        28.08        27.72       357.37        40.27         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT 
       32.75        23.93       101.26        74.73        11.41        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 
       26.56        49.48        27.09        27.02        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO 
      174.84        12.43        77.88         0.20        47.54         7.23 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       11.74       117.93        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB 
       39.58        12.62        50.10        21.37        59.41       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 
      294.77         6.67        18.05         0.33         0.69        63.02 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       42.08       105.04        24.03        54.38         8.61        90.28 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.41        52.34         3.75        22.68        30.18        10.36 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
       15.16        36.03        14.43 

$`AMP PEAK  8(6P24.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       17.03        12.99       112.04       112.57        71.80        28.08 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH 
       43.43       103.10       115.53        86.76        11.87        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       12.10       171.58        56.19        59.57       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51F 
       46.32       166.52        60.23        24.53         9.34        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR 
       56.35       145.12        22.62        63.81       125.79       178.32 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GM 
       18.18        30.84        79.59        15.19        58.52        95.24 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
      129.63       117.17         6.41        11.34        22.29        25.18 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       36.03       117.21       107.34        61.18        53.92        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV 
       28.60       215.44        15.68        10.16        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       12.20        29.82        14.70       151.27        91.56        13.55 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       47.84        63.78        64.64        56.84        18.61        37.35 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      369.93       195.02        46.82       102.90        36.82        86.14 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO 
       67.43       161.03        48.72        54.74        75.48       126.81 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2ML 
       21.67        19.76        61.51       103.20        16.96       203.05 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AH 
      134.40        71.21       122.73        51.62        54.51       138.81 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       109.58        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A1A1 
       77.75        98.40       268.93       152.35       131.51        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A42K TCGA-FR-A3YN 
       23.34        20.15        31.27        32.05         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z7 
      174.21         7.00        38.27        94.39       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 
       19.30         9.90         2.04       139.89        84.72        46.36 
TCGA-HR-A2OH TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 
       65.88       212.22       121.08         4.01       219.16        38.56 
TCGA-WE-A8ZN TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       56.98        43.73         2.20        23.64        93.07        11.74 

  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                        369.93 
  AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE 
                       47.540                        54.215 
[1] "0.2 - 357.4 (47.5)" "0.2 - 369.9 (54.2)"
[1] "hr=" "1.4"
D8V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  8(6P24.3) MUTATED                   42             4
  AMP PEAK  8(6P24.3) WILD-TYPE                 19             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  8(6P24.3) MUTATED                                          45
  AMP PEAK  8(6P24.3) WILD-TYPE                                        27
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK  8(6P24.3) MUTATED                   107
  AMP PEAK  8(6P24.3) WILD-TYPE                 102
D8V4, multiclass
                                           clus
vv                                          AMP PEAK  8(6P24.3) MUTATED
  DISTANT METASTASIS                                                 42
  PRIMARY TUMOR                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          45
  REGIONAL LYMPH NODE                                               107
                                           clus
vv                                          AMP PEAK  8(6P24.3) WILD-TYPE
  DISTANT METASTASIS                                                   19
  PRIMARY TUMOR                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            27
  REGIONAL LYMPH NODE                                                 102
[1] 4 2
[1] 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             4       3      17        7       18
  AMP PEAK  8(6P24.3) WILD-TYPE           8       4      11       10        9
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  8(6P24.3) MUTATED         15         7         9         9
  AMP PEAK  8(6P24.3) WILD-TYPE        7         7        10         3
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  8(6P24.3) MUTATED          17         13         21         29
  AMP PEAK  8(6P24.3) WILD-TYPE        18          2         11         29
                               vv
clus                            STAGE IV
  AMP PEAK  8(6P24.3) MUTATED         11
  AMP PEAK  8(6P24.3) WILD-TYPE        8
D8V5, multiclass
             clus
vv            AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  I OR II NOS                           4                             8
  STAGE 0                               3                             4
  STAGE I                              17                            11
  STAGE IA                              7                            10
  STAGE IB                             18                             9
  STAGE II                             15                             7
  STAGE IIA                             7                             7
  STAGE IIB                             9                            10
  STAGE IIC                             9                             3
  STAGE III                            17                            18
  STAGE IIIA                           13                             2
  STAGE IIIB                           21                            11
  STAGE IIIC                           29                            29
  STAGE IV                             11                             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  8(6P24.3) MUTATED      30 41 42 47
  AMP PEAK  8(6P24.3) WILD-TYPE    33 30 32 20
D8V6, multiclass
       clus
vv      AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  T0+T1                          30                            33
  T2                             41                            30
  T3                             42                            32
  T4                             47                            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
  AMP PEAK  8(6P24.3) MUTATED   95 36 23 25
  AMP PEAK  8(6P24.3) WILD-TYPE 73 25 15 22
D8V7, multiclass
    clus
vv   AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  N0                          95                            73
  N1                          36                            25
  N2                          23                            15
  N3                          25                            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
  AMP PEAK  8(6P24.3) MUTATED   171   3   3   2   4
  AMP PEAK  8(6P24.3) WILD-TYPE 135   1   0   2   5
D8V8, multiclass
     clus
vv    AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  M0                          171                           135
  M1                            3                             1
  M1A                           3                             0
  M1B                           2                             2
  M1C                           4                             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"
D8V9, binary
                               cls
clus                             0  1
  AMP PEAK  8(6P24.3) MUTATED   73 53
  AMP PEAK  8(6P24.3) WILD-TYPE 56 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED     73   53
  AMP PEAK  8(6P24.3) WILD-TYPE   56   34
     clus
vv    AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  NO                           73                            56
  YES                          53                            34
[1] 2 2
[1] FALSE
D8V10, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P24.3) MUTATED    25 174
  AMP PEAK  8(6P24.3) WILD-TYPE  18 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED     25  174
  AMP PEAK  8(6P24.3) WILD-TYPE   18  130
     clus
vv    AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  NO                           25                            18
  YES                         174                           130
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P24.3) MUTATED    78 121
  AMP PEAK  8(6P24.3) WILD-TYPE  53  96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED     78  121
  AMP PEAK  8(6P24.3) WILD-TYPE   53   96
        clus
vv       AMP PEAK  8(6P24.3) MUTATED AMP PEAK  8(6P24.3) WILD-TYPE
  FEMALE                          78                            53
  MALE                           121                            96
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P24.3) MUTATED       3                         1   184
  AMP PEAK  8(6P24.3) WILD-TYPE     2                         0   142
D8V13, multiclass
                           clus
vv                          AMP PEAK  8(6P24.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             184
                           clus
vv                          AMP PEAK  8(6P24.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               142
[1] 3 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     4 192
  AMP PEAK  8(6P24.3) WILD-TYPE   3 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P24.3) MUTATED      4  192
  AMP PEAK  8(6P24.3) WILD-TYPE    3  142
                        clus
vv                       AMP PEAK  8(6P24.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         192
                        clus
vv                       AMP PEAK  8(6P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           142
[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    35  36
  AMP PEAK  9(6Q12) WILD-TYPE 133 129
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         71                         262 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         36                         129 
$`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        44.19        61.38 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EC 
       26.37        93.21        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        60.23        51.12        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        53.16        52.67         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-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZM 
        6.58        22.49         4.70        23.80         7.30        47.38 
TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A266 
       27.39        14.20         0.13         7.23        11.61        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-AA1V 
       16.24        15.42        14.50        14.50        14.50        10.98 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-YG-AA3P 
       71.01        11.84         3.72        21.83         4.70 

$`AMP PEAK  9(6Q12) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97        16.47       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       85.32        88.50        68.22        86.76        11.41         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        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
      114.67        15.25        46.98        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F 
       24.00         6.31         9.34       103.59        29.23        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC 
      110.24        52.01        13.68        17.72        29.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       10.22        15.19         4.18       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       75.65       124.47        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW 
        4.01        21.93         5.72        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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       19.00        13.35        11.57         6.31         8.12         1.35 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31         4.34        15.85         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        39.62         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        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       28.31        55.69         5.42         1.15        13.02        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73        44.25         7.96        63.42       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AC 
       56.02        26.99        21.60        60.49       122.73        51.62 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JB 
       30.15        13.81        15.95        12.72        22.92         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F 
       12.95        38.40        76.41        25.18        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A19W 
      114.15        34.88         4.21        13.45         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL 
       78.44         1.87        12.62        11.74         9.04         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
        5.36        13.28         2.20         3.29        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       11.01        14.24        15.52         7.33         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-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.89        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
        8.68         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
        0.99         0.16        17.33         9.90         0.85        44.28 
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-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       15.81         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       164.19         8.98        60.03         2.99       185.16 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        5.49         6.48         7.10        18.67        21.07        13.12 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.42         5.36         1.08        19.96         1.94        12.07 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         8.22         6.67         5.98 

  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                       0.13                        0.13 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                     124.31                      185.16 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                     14.560                      14.765 
[1] "0.1 - 124.3 (14.6)" "0.1 - 185.2 (14.8)"
[1] "hr=" "1.1"
D9V2, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q12) MUTATED    38  36
  AMP PEAK  9(6Q12) WILD-TYPE 135 130
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         74                         265 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         36                         130 
$`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        62.07        86.93 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW 
       39.75       174.84       137.92       125.19        54.67         3.65 
TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EB-A5UN 
       18.12         9.90        66.25        48.89       194.83        52.01 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
       12.20        27.22        33.73        26.89        68.15       133.81 
TCGA-EE-A2GB TCGA-EE-A2GN TCGA-EE-A2GT TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MN 
       59.28        90.97        44.88       103.27       204.66        47.54 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J3 
      162.48        71.21        53.26       124.31         3.68       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19C 
       36.95        64.08        34.32        53.19         9.17        48.89 
TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       12.59        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A8YD 
       43.82        20.15        16.37        80.32        46.98        29.46 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TU 
      202.65        27.72       101.26        49.48       174.84        47.54 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK 
        7.23        11.74        10.13        64.44        62.79        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZQ 
       21.37        59.41        42.08       105.04        24.03        52.34 
TCGA-WE-A8ZX TCGA-YG-AA3P 
       22.68        14.43 

$`AMP PEAK  9(6Q12) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
      103.10       115.53       168.00        86.76        11.87       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        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
      130.72        58.06        46.98        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F 
       24.53        13.87         9.34       103.59        45.30        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC 
      125.79       135.75       178.32        18.18        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       11.61        15.19        58.52       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       95.24       161.00       137.79        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
      151.53         6.41        11.34        22.29        11.11        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        68.25        54.02        17.29         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        91.56 
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 
       63.78        72.07        64.64         2.60        56.84        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       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       268.73       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       158.63       203.05       167.90       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      134.40       122.73        51.62        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      138.81       127.20       201.80        27.35        51.35       109.58 
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-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG 
      131.51         8.88       148.18        79.99        23.34        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       210.08        15.16         7.00        38.27        34.82 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       94.39       216.92        48.59       228.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        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-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        22.92         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A 
        9.90         2.04       139.89       117.93        84.72        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       39.58        46.36        12.62        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        6.67        18.05         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      121.08         4.01       219.16        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       90.28        56.98        59.41         3.75        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       30.18        10.36        15.16        36.03        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  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                      369.93 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                      49.79                       50.76 
[1] "3.6 - 204.7 (49.8)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.1"
D9V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  9(6Q12) MUTATED                   15             3
  AMP PEAK  9(6Q12) WILD-TYPE                 46             2
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK  9(6Q12) MUTATED                                          18
  AMP PEAK  9(6Q12) WILD-TYPE                                        54
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  9(6Q12) MUTATED                    40
  AMP PEAK  9(6Q12) WILD-TYPE                 169
D9V4, multiclass
                                           clus
vv                                          AMP PEAK  9(6Q12) MUTATED
  DISTANT METASTASIS                                               15
  PRIMARY TUMOR                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        18
  REGIONAL LYMPH NODE                                              40
                                           clus
vv                                          AMP PEAK  9(6Q12) WILD-TYPE
  DISTANT METASTASIS                                                 46
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          54
  REGIONAL LYMPH NODE                                               169
[1] 4 2
[1] 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       6        4       11
  AMP PEAK  9(6Q12) WILD-TYPE          11       4      22       13       16
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  9(6Q12) MUTATED          5         3         3         5         5
  AMP PEAK  9(6Q12) WILD-TYPE       17        11        16         7        30
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  9(6Q12) MUTATED            6          8          6        0
  AMP PEAK  9(6Q12) WILD-TYPE          9         24         52       19
D9V5, multiclass
             clus
vv            AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  I OR II NOS                         1                          11
  STAGE 0                             3                           4
  STAGE I                             6                          22
  STAGE IA                            4                          13
  STAGE IB                           11                          16
  STAGE II                            5                          17
  STAGE IIA                           3                          11
  STAGE IIB                           3                          16
  STAGE IIC                           5                           7
  STAGE III                           5                          30
  STAGE IIIA                          6                           9
  STAGE IIIB                          8                          24
  STAGE IIIC                          6                          52
  STAGE IV                            0                          19
[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      14 18 11 19
  AMP PEAK  9(6Q12) WILD-TYPE    49 53 63 48
D9V6, multiclass
       clus
vv      AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  T0+T1                        14                          49
  T2                           18                          53
  T3                           11                          63
  T4                           19                          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  9(6Q12) MUTATED    39  13   7   6
  AMP PEAK  9(6Q12) WILD-TYPE 129  48  31  41
D9V7, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  N0                        39                         129
  N1                        13                          48
  N2                         7                          31
  N3                         6                          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                           M0  M1 M1A M1B M1C
  AMP PEAK  9(6Q12) MUTATED    68   0   0   0   0
  AMP PEAK  9(6Q12) WILD-TYPE 238   4   3   4   9
D9V8, multiclass
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  M0                         68                         238
  M1                          0                           4
  M1A                         0                           3
  M1B                         0                           4
  M1C                         0                           9
[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   34 17
  AMP PEAK  9(6Q12) WILD-TYPE 95 70
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     34   17
  AMP PEAK  9(6Q12) WILD-TYPE   95   70
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                         34                          95
  YES                        17                          70
[1] 2 2
[1] FALSE
D9V10, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED    10  66
  AMP PEAK  9(6Q12) WILD-TYPE  33 238
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     10   66
  AMP PEAK  9(6Q12) WILD-TYPE   33  238
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                         10                          33
  YES                        66                         238
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED    25  51
  AMP PEAK  9(6Q12) WILD-TYPE 106 166
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     25   51
  AMP PEAK  9(6Q12) WILD-TYPE  106  166
        clus
vv       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  FEMALE                        25                         106
  MALE                          51                         166
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6Q12) MUTATED       2                         0    70
  AMP PEAK  9(6Q12) WILD-TYPE     3                         1   256
D9V13, multiclass
                           clus
vv                          AMP PEAK  9(6Q12) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            70
                           clus
vv                          AMP PEAK  9(6Q12) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             256
[1] 3 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     1  73
  AMP PEAK  9(6Q12) WILD-TYPE   6 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED      1   73
  AMP PEAK  9(6Q12) WILD-TYPE    6  261
                        clus
vv                       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                        73                         261
[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   96 91
  AMP PEAK 10(7P22.1) WILD-TYPE 72 74
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          187                           146 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                           91                            74 
$`AMP PEAK 10(7P22.1) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97        16.47         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       70.16        22.55        21.14        88.50        86.76        11.41 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       92.42        56.19        59.57       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       82.29        61.38         6.31         9.34       103.59        26.37 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       54.31        21.44        32.61        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GN 
       23.11        22.06        10.22         4.18       108.79       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       87.62        11.44        21.93         9.90        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       14.60        48.79        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
        9.99        44.52        36.69        25.15         4.93         6.64 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       17.56        13.15         0.20         0.13        13.35        13.22 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B 
        0.20        10.55         6.31         8.12         1.12        60.23 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        9.21         7.99        37.97        11.15        62.79         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
        9.50        12.03         8.09        30.44        32.15        11.31 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       36.33        51.12        60.00        47.21        30.08        19.43 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 
       35.54        28.31        33.83        55.69         5.42         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
       98.27         2.70        63.42       125.65        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        21.60        60.49        53.16         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-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19B 
        3.22        22.92        21.60         0.95         5.72        25.18 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
        3.78        11.90       114.15        34.88         4.21        28.60 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL 
       34.68        36.07         6.58         1.87        22.49         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        64.47 
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-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY 
       30.87        12.89        47.38         8.65         8.81         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY 
        5.23         3.22        28.73        14.20         0.20        17.33 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        7.23        11.61        31.33        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1V 
       14.50        15.81         5.79        18.05         2.99        10.98 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      185.16        71.01        11.84         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       18.67         3.72        21.83         1.08         1.94         6.18 
TCGA-YG-AA3P 
        4.70 

$`AMP PEAK 10(7P22.1) WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
        6.97       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       85.32         8.38        68.22        44.19         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV 
        6.31        64.44        15.25        13.32        24.00        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL 
       93.21        54.74        31.30        32.28        25.78       110.24 
TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM 
       47.87        29.72        15.19       142.45        38.93        75.65 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB 
        5.56        24.07         4.01         5.72        39.19        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X 
       19.36         7.00        14.83        23.15        19.00        11.57 
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        15.85 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R 
        1.18         9.90         8.55        36.85        39.62         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         2.43         8.09        49.22        36.30         9.67 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       34.29        17.98        16.01         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       36.33         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AC 
       44.25         7.96        14.56       111.91        52.67        51.62 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35        18.41        21.73 
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-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
        3.52        11.11        13.45        42.84         9.57        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-A3ET TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA 
        9.04         6.58         3.45        11.01        23.80         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZS 
        3.39        11.08         7.17        12.92        52.08        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       40.64         8.68        27.39        53.85         7.36        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.99         0.13         0.16 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-LH-A9QB TCGA-OD-A75X 
        9.90         0.85        44.28        84.72         0.43        11.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-WE-A8ZN 
        0.33         0.69       164.19         8.98        60.03        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT 
       13.12         3.42         5.36        19.96        12.07         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                         0.13                          0.13 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       185.16                        164.19 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       14.700                        14.695 
[1] "0.1 - 185.2 (14.7)" "0.1 - 164.2 (14.7)"
[1] "hr=" "1.1"
D10V2, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(7P22.1) MUTATED   98 92
  AMP PEAK 10(7P22.1) WILD-TYPE 75 74
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                          190                           149 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                           92                            74 
$`AMP PEAK 10(7P22.1) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       71.80        31.59        23.77       115.53        86.76        11.87 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        56.19        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        86.93        13.87         9.34       103.59        39.75 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
      145.12        22.62        63.81       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GN 
      125.19        79.59        11.61        58.52       170.20       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 
      137.79        29.06       151.53        54.67         6.41        22.29 
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-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-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       53.92        65.92        68.09       215.44        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
       17.85        17.29        52.01        12.20        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       94.98        33.73       133.81       168.26        63.35        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.97        63.78         2.60        18.61        56.42        37.35 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      369.93       195.02        46.82        86.14        59.28       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        48.72        89.33        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ 
      126.81        13.91        21.67       129.27        28.83        96.23 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      158.63       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        53.26       124.31       122.73         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        23.47       138.81       172.18       127.20        64.08 
TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G 
      201.80         9.17        98.40        48.89        13.02       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T 
      152.35         6.44        61.05       162.08        37.25         8.88 
TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       23.34        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       210.08        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       29.46        94.39       216.92        20.91        28.08         7.79 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
      357.37        53.52        40.27        32.75        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 
      133.55        11.41        27.09        27.02        50.14        28.73 
TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
      174.84         0.20        19.30         7.23        11.74       117.93 
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 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS 
       12.62        50.10        21.37        59.41        65.88         6.67 
TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       18.05         4.01        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       38.56        54.38         8.61        90.28        52.34        22.68 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        10.36        36.03        14.43 

$`AMP PEAK 10(7P22.1) WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       12.99       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      103.10        65.49       168.00        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV 
       12.10        66.08        58.06        60.23        24.53        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL 
      174.84        55.73        56.35        32.94        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM 
      137.92        30.84        15.19       228.99        89.13        95.24 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      129.63       117.17         3.65        18.12        11.34        11.11 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5SG 
      194.83        23.44        28.60        10.49        15.68        68.25 
TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       54.02         6.35        29.82        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G 
        4.96       151.27        91.56        13.55        80.61        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       64.64        56.84        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-A2GK 
      102.90        36.82        39.29        67.43       314.56        54.74 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MC 
       14.30        55.59        44.88        94.82        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
      203.05        71.21        51.62        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        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L 
       13.94        50.76        77.75        12.59        26.37       131.51 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       44.05        50.89       148.18        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FS-A1YX 
       16.37        31.27        32.05       247.04        80.32        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZG 
      228.59       202.65        27.72        48.85        15.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38        74.73       148.80        53.16        26.56        49.48 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       77.82        66.67        12.43        26.73        49.45        77.88 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       22.92        47.54         0.16         9.90         2.04       139.89 
TCGA-GN-A265 TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       84.72       357.04       294.77         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       63.02       121.08        56.98        59.41         3.75        43.73 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       30.18        15.16        23.64        93.07        11.74 

  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 
                       369.93                        357.04 
  AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE 
                       49.495                        50.890 
[1] "0.2 - 369.9 (49.5)" "0.2 - 357.0 (50.9)"
[1] "hr=" "1"  
D10V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 10(7P22.1) MUTATED                   33             4
  AMP PEAK 10(7P22.1) WILD-TYPE                 28             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 10(7P22.1) MUTATED                                          39
  AMP PEAK 10(7P22.1) WILD-TYPE                                        33
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK 10(7P22.1) MUTATED                   119
  AMP PEAK 10(7P22.1) WILD-TYPE                  90
D10V4, multiclass
                                           clus
vv                                          AMP PEAK 10(7P22.1) MUTATED
  DISTANT METASTASIS                                                 33
  PRIMARY TUMOR                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          39
  REGIONAL LYMPH NODE                                               119
                                           clus
vv                                          AMP PEAK 10(7P22.1) WILD-TYPE
  DISTANT METASTASIS                                                   28
  PRIMARY TUMOR                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            33
  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 10(7P22.1) MUTATED             9       1      16        9       10
  AMP PEAK 10(7P22.1) WILD-TYPE           3       6      12        8       17
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 10(7P22.1) MUTATED         13         8         8        10
  AMP PEAK 10(7P22.1) WILD-TYPE        9         6        11         2
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 10(7P22.1) MUTATED          23         10         19         33
  AMP PEAK 10(7P22.1) WILD-TYPE        12          5         13         25
                               vv
clus                            STAGE IV
  AMP PEAK 10(7P22.1) MUTATED         11
  AMP PEAK 10(7P22.1) WILD-TYPE        8
D10V5, multiclass
             clus
vv            AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  I OR II NOS                           9                             3
  STAGE 0                               1                             6
  STAGE I                              16                            12
  STAGE IA                              9                             8
  STAGE IB                             10                            17
  STAGE II                             13                             9
  STAGE IIA                             8                             6
  STAGE IIB                             8                            11
  STAGE IIC                            10                             2
  STAGE III                            23                            12
  STAGE IIIA                           10                             5
  STAGE IIIB                           19                            13
  STAGE IIIC                           33                            25
  STAGE IV                             11                             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 10(7P22.1) MUTATED      41 35 41 39
  AMP PEAK 10(7P22.1) WILD-TYPE    22 36 33 28
D10V6, multiclass
       clus
vv      AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  T0+T1                          41                            22
  T2                             35                            36
  T3                             41                            33
  T4                             39                            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 10(7P22.1) MUTATED   89 36 21 32
  AMP PEAK 10(7P22.1) WILD-TYPE 79 25 17 15
D10V7, multiclass
    clus
vv   AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  N0                          89                            79
  N1                          36                            25
  N2                          21                            17
  N3                          32                            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  AMP PEAK 10(7P22.1) MUTATED   171   3   3   1   5
  AMP PEAK 10(7P22.1) WILD-TYPE 135   1   0   3   4
D10V8, multiclass
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  M0                          171                           135
  M1                            3                             1
  M1A                           3                             0
  M1B                           1                             3
  M1C                           5                             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"
D10V9, binary
                               cls
clus                             0  1
  AMP PEAK 10(7P22.1) MUTATED   73 48
  AMP PEAK 10(7P22.1) WILD-TYPE 56 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     73   48
  AMP PEAK 10(7P22.1) WILD-TYPE   56   39
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                           73                            56
  YES                          48                            39
[1] 2 2
[1] FALSE
D10V10, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED    29 165
  AMP PEAK 10(7P22.1) WILD-TYPE  14 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     29  165
  AMP PEAK 10(7P22.1) WILD-TYPE   14  139
     clus
vv    AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  NO                           29                            14
  YES                         165                           139
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P22.1) MUTATED    73 122
  AMP PEAK 10(7P22.1) WILD-TYPE  58  95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED     73  122
  AMP PEAK 10(7P22.1) WILD-TYPE   58   95
        clus
vv       AMP PEAK 10(7P22.1) MUTATED AMP PEAK 10(7P22.1) WILD-TYPE
  FEMALE                          73                            58
  MALE                           122                            95
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7P22.1) MUTATED       5                         0   180
  AMP PEAK 10(7P22.1) WILD-TYPE     0                         1   146
D10V13, multiclass
                           clus
vv                          AMP PEAK 10(7P22.1) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             180
                           clus
vv                          AMP PEAK 10(7P22.1) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               146
[1] 3 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     5 185
  AMP PEAK 10(7P22.1) WILD-TYPE   2 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.1) MUTATED      5  185
  AMP PEAK 10(7P22.1) WILD-TYPE    2  149
                        clus
vv                       AMP PEAK 10(7P22.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         185
                        clus
vv                       AMP PEAK 10(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           149
[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   105  97
  AMP PEAK 11(7Q34) WILD-TYPE  63  68
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        202                         131 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                         97                          68 
$`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        86.76        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        59.57        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        29.23        93.21        54.31        21.44 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       32.61        52.01        13.68        17.72        23.11        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN 
       22.06        10.22         4.18       108.79        75.65       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6E9 
       87.62        11.44         5.56        24.07        21.93         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-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
        4.93         6.64        17.56        14.83        13.15         0.13 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       13.35        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        60.23         9.21         7.99        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       62.79        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       30.44        32.15        11.31        36.33        51.12        60.00 
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        55.69         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 
      125.65        56.02        21.60        60.49        53.16         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-A3JB TCGA-EE-A3JD 
        3.22        22.92        21.60        21.60         0.95        27.35 
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-A19T TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET 
        9.57        36.07         6.58         1.87        13.08         6.58 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        1.71         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX 
        5.36        13.28         2.20         4.70         3.29         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-A1ZU 
       30.87        47.38         8.65         8.81        49.15         8.68 
TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 
        5.23         3.22         7.36        28.73        14.20         0.20 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
       17.33         7.23        11.61        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK 
       16.24        15.42        12.16        14.70        10.65        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1O 
       14.50        15.81         0.43         5.79        18.05         2.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      185.16        71.01        11.84         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 
       18.67        21.07         3.72        21.83         1.08         1.94 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.18         4.70         8.22         6.67 

$`AMP PEAK 11(7Q34) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        3.02         6.97         6.97       111.09       110.79        28.08 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JK 
       81.24        10.29         8.38        68.22        44.19         6.31 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
       64.44       114.67        24.00        54.74        31.30        32.28 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL 
       25.78       110.24        47.87        15.19       142.45        38.93 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
        4.01         5.72        39.19        22.36        19.36         7.00 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A184 
        0.20        23.15        19.00        11.57         6.31         5.13 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D 
        4.31         4.34        15.85         1.18         9.90        11.15 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        8.55         8.09         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-A2GJ 
       49.22        36.30         9.67        34.29        17.98        19.43 
TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
       16.01        33.83         1.15        13.02        36.33         8.84 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       47.51         9.53        29.46         2.73        44.25        14.56 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD 
      111.91        25.08        26.99        52.67        51.62         3.68 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       16.14        22.22        18.41        21.73        33.60        18.61 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19W 
       76.41         3.52        11.11        13.45        42.84        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       78.44        11.80         1.51        12.62        11.74         9.04 
TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       22.49         3.58        64.47        11.01        14.24        15.52 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
        7.30         3.39        19.53        12.92        12.89        52.08 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FB 
       40.64        27.39         0.82        53.85        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT 
        6.41         2.27         0.99         0.13         0.16         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A693 
        0.85        44.28        11.84        14.50        11.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8ZO 
        0.69       164.19         8.98        60.03        10.98        13.12 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3V 
        3.42         5.36        19.96        12.07         5.98 

  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                       0.13                        0.13 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                     185.16                      164.19 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                      15.57                       13.45 
[1] "0.1 - 185.2 (15.6)" "0.1 - 164.2 (13.4)"
[1] "hr=" "1.2"
D11V2, survival
                             sevent
clus2                           0   1
  AMP PEAK 11(7Q34) MUTATED   108  98
  AMP PEAK 11(7Q34) WILD-TYPE  65  68
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                        206                         133 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                         98                          68 
$`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        86.76        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        59.57        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        45.30       174.84       145.12        22.62 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       63.81       135.75       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN 
       79.59        11.61        58.52       170.20        95.24       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      137.79        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        3.65         6.41        22.29         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-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
      215.44        15.68        13.87        17.85        17.29        52.01 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       12.20        27.22        94.98        33.73        14.70        26.89 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
      133.81       168.26        63.35        47.84        63.78        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W 
        2.60        56.84        18.61        56.42       369.93       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       46.82        86.14        59.28       161.03       208.04        48.72 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M6 
       79.66        75.48       126.81        13.91        44.88       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       28.83        19.76        16.96        96.23       158.63       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       134.40       162.48        53.26       124.31       122.73 
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-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A197 
       36.95        64.08       201.80        27.35        31.40        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G 
       50.76         9.17        98.40        48.89        13.02       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      152.35         6.44        61.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K 
        8.88        23.34        16.37        80.32        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA 
       92.98       174.21        15.72       210.08         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z7 
       34.82        29.46        94.39        48.59       202.65         7.79 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM 
      357.37        53.52        15.45         9.70        32.75       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F2 
      133.55        11.41       148.80        26.56        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        19.30         7.23 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       11.74       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH 
       32.48        39.58        12.62        50.10        59.41        65.88 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 
      357.04         6.67        18.05         4.01       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        38.56        54.38         8.61        90.28        56.98 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
       52.34        22.68         2.20        10.36        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
       23.64        93.07 

$`AMP PEAK 11(7Q34) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       17.03        61.02        12.99       112.04       133.25        28.08 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JK 
       95.74        43.43        65.49       168.00        62.07        12.10 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CF TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
       66.08       130.72        24.53        55.73        56.35        32.94 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL 
       26.89       125.79       137.92        15.19       228.99        89.13 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 
       18.12        11.34        11.11       194.83        23.44        28.60 
TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X 
       10.49        10.16        68.25        54.02         6.35        29.82 
TCGA-EE-A17Z TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
        8.65        68.15         4.96       151.27        91.56        13.55 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       80.61        13.97        72.07        37.35        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        36.82        39.29        67.43 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
      314.56        89.33        54.74        90.97        14.30        55.59 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       94.82        21.67        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT 
      103.20       204.66       203.05        47.54       248.65        71.21 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       51.62         3.68        34.32        53.19        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L 
      148.08        35.44        77.75        12.59        26.37       131.51 
TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       44.05       148.18        79.99        43.82        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05       247.04        46.98        15.16       216.92       228.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ 
       20.91        28.08        27.72        48.85        40.27        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
       23.93        74.73        53.16        49.48        27.09        77.82 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88        22.92        47.54 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U8 TCGA-GN-A8LL 
        0.16         9.90         2.04       139.89        46.36        21.37 
TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
      294.77         0.33         0.69       212.22        63.02       121.08 
TCGA-W3-AA1V TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       42.08        59.41         3.75        43.73        30.18        15.16 
TCGA-Z2-AA3V 
       11.74 

  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 
                     369.93                      314.56 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                      52.80                       47.54 
[1] "0.2 - 369.9 (52.8)" "0.2 - 314.6 (47.5)"
[1] "hr=" "1.1"
D11V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 11(7Q34) MUTATED                   32             5
  AMP PEAK 11(7Q34) WILD-TYPE                 29             0
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 11(7Q34) MUTATED                                          47
  AMP PEAK 11(7Q34) WILD-TYPE                                        25
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK 11(7Q34) MUTATED                   128
  AMP PEAK 11(7Q34) WILD-TYPE                  81
D11V4, multiclass
                                           clus
vv                                          AMP PEAK 11(7Q34) MUTATED
  DISTANT METASTASIS                                               32
  PRIMARY TUMOR                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        47
  REGIONAL LYMPH NODE                                             128
                                           clus
vv                                          AMP PEAK 11(7Q34) WILD-TYPE
  DISTANT METASTASIS                                                 29
  PRIMARY TUMOR                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          25
  REGIONAL LYMPH NODE                                                81
[1] 4 2
[1] 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            12       3      15       10       13
  AMP PEAK 11(7Q34) WILD-TYPE           0       4      13        7       14
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 11(7Q34) MUTATED         11         8         8        10        26
  AMP PEAK 11(7Q34) WILD-TYPE       11         6        11         2         9
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 11(7Q34) MUTATED           12         22         34       10
  AMP PEAK 11(7Q34) WILD-TYPE          3         10         24        9
D11V5, multiclass
             clus
vv            AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  I OR II NOS                        12                           0
  STAGE 0                             3                           4
  STAGE I                            15                          13
  STAGE IA                           10                           7
  STAGE IB                           13                          14
  STAGE II                           11                          11
  STAGE IIA                           8                           6
  STAGE IIB                           8                          11
  STAGE IIC                          10                           2
  STAGE III                          26                           9
  STAGE IIIA                         12                           3
  STAGE IIIB                         22                          10
  STAGE IIIC                         34                          24
  STAGE IV                           10                           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 11(7Q34) MUTATED      43 38 46 42
  AMP PEAK 11(7Q34) WILD-TYPE    20 33 28 25
D11V6, multiclass
       clus
vv      AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  T0+T1                        43                          20
  T2                           38                          33
  T3                           46                          28
  T4                           42                          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 11(7Q34) MUTATED   97 42 25 32
  AMP PEAK 11(7Q34) WILD-TYPE 71 19 13 15
D11V7, multiclass
    clus
vv   AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  N0                        97                          71
  N1                        42                          19
  N2                        25                          13
  N3                        32                          15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B M1C
  AMP PEAK 11(7Q34) MUTATED   189   2   3   1   5
  AMP PEAK 11(7Q34) WILD-TYPE 117   2   0   3   4
D11V8, multiclass
     clus
vv    AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  M0                        189                         117
  M1                          2                           2
  M1A                         3                           0
  M1B                         1                           3
  M1C                         5                           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"
D11V9, binary
                             cls
clus                           0  1
  AMP PEAK 11(7Q34) MUTATED   83 52
  AMP PEAK 11(7Q34) WILD-TYPE 46 35
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     83   52
  AMP PEAK 11(7Q34) WILD-TYPE   46   35
     clus
vv    AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  NO                         83                          46
  YES                        52                          35
[1] 2 2
[1] FALSE
D11V10, binary
                             cls
clus                            0   1
  AMP PEAK 11(7Q34) MUTATED    29 183
  AMP PEAK 11(7Q34) WILD-TYPE  14 121
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     29  183
  AMP PEAK 11(7Q34) WILD-TYPE   14  121
     clus
vv    AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  NO                         29                          14
  YES                       183                         121
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, binary
                             cls
clus                            0   1
  AMP PEAK 11(7Q34) MUTATED    89 124
  AMP PEAK 11(7Q34) WILD-TYPE  42  93
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     89  124
  AMP PEAK 11(7Q34) WILD-TYPE   42   93
        clus
vv       AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  FEMALE                        89                          42
  MALE                         124                          93
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q34) MUTATED       4                         0   198
  AMP PEAK 11(7Q34) WILD-TYPE     1                         1   128
D11V13, multiclass
                           clus
vv                          AMP PEAK 11(7Q34) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                           198
                           clus
vv                          AMP PEAK 11(7Q34) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             128
[1] 3 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     4 203
  AMP PEAK 11(7Q34) WILD-TYPE   3 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED      4  203
  AMP PEAK 11(7Q34) WILD-TYPE    3  131
                        clus
vv                       AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       203                         131
[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   81 72
  AMP PEAK 12(8Q11.21) WILD-TYPE 87 93
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                           153                            180 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                            72                             93 
$`AMP PEAK 12(8Q11.21) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
        6.97        16.47        70.16        81.24        10.29        85.32 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       88.50        86.76        44.19        56.19        64.44        59.57 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       15.25        82.29        61.38        13.32       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A5GR 
       29.23        93.21        54.31        32.28        52.01        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D9-A6EA 
       17.72        23.11         4.18       142.45        87.62        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-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
        9.99        17.56        13.15         0.20         0.13        23.15 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B 
       19.00         0.20        10.55         6.31         1.12        60.23 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       37.97        62.79         8.55         8.84        30.44         2.43 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM 
        9.67        17.98        60.00        47.21        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       33.83        55.69         5.42        98.27         2.70         6.18 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB 
        2.73         7.96        25.08        60.49       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        30.15        15.95         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       21.60        22.22        12.95         3.78       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19T 
        4.21        13.45        28.60        42.84        36.07         6.58 
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-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YX 
        6.71         3.58         5.36        13.28         4.70         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZK 
       23.80        15.52         7.33        20.38         8.22        12.89 
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-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        8.68         0.82         3.22         7.36        28.73        14.20 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 
        5.98         2.27         0.20         0.16         9.90        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A8LL 
       84.72        10.13        16.24        12.16        14.70        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       14.50        15.81        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM 
        0.69       164.19         8.98        71.01         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YG-AA3O 
       21.07         3.72         3.42        21.83         1.94         6.18 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         6.67         5.98 

$`AMP PEAK 12(8Q11.21) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
        3.02         6.97         8.52       111.09        32.42       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       28.08        22.55        45.83         8.38        21.14        68.22 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ 
       11.41         7.50        36.16         6.31        92.42       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51F 
       46.98        46.32        24.00         6.31         9.34        54.74 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       31.30        21.44        32.61        25.78       110.24        47.87 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL 
       29.72        22.06        10.22        15.19       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
       75.65       124.47        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 
       21.93         5.72         9.90        48.79        10.03        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-A3F8 TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 
        7.00        14.83        13.35        13.22        11.57         8.12 
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        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H 
        9.21         1.18         7.99         9.90        11.15        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        1.08        39.62         9.50        12.03         8.09         9.99 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       32.15         8.09        11.31        49.22        36.30        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR 
       51.12        34.29        30.08        19.43        16.01         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       13.02        34.98        36.33         8.84        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25        14.56        63.42       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       56.02        26.99        21.60        53.16        52.67         5.56 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
       51.62        13.81        12.72        16.14         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       18.41        21.73        33.60        31.40        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-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG 
       34.68         9.57        17.72        78.44         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P 
       11.74         9.04         1.71         5.62        18.41        15.72 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZA 
        2.20         3.29        64.47        11.01        14.24         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        3.39        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       27.39         5.23        53.85        10.78         6.41         0.99 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
        0.13        17.33         7.23         0.85        11.61        44.28 
TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-W3-A828 
       15.42        11.84        10.65        14.50         0.43        60.03 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
        2.99        10.98       185.16        11.84         5.49         6.48 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT 
       13.12         5.36         1.08        19.96        12.07         8.22 

  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                          0.13                           0.13 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                        164.19                         185.16 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                         15.25                          14.53 
[1] "0.1 - 164.2 (15.2)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.1"
D12V2, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(8Q11.21) MUTATED   81 72
  AMP PEAK 12(8Q11.21) WILD-TYPE 92 94
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                           153                            186 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                            72                             94 
$`AMP PEAK 12(8Q11.21) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       12.99        16.57        71.80        95.74        43.43       103.10 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      115.53        86.76        62.07        56.19        66.08        59.57 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       58.06       166.52        86.93        60.23       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A5GR 
       45.30       174.84       145.12        32.94       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D9-A6EA 
       18.18       125.19        58.52       228.99       137.79        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       66.25        22.95        36.03       117.21       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       35.93       215.44        13.87        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B 
       54.02        12.20        27.22         8.65        33.73       133.81 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       47.84        63.78        72.07        14.47       369.93        25.87 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM 
       39.29       314.56       161.03       208.04        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       90.97       126.81        13.91       129.27        28.83        19.76 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB 
      268.73        16.96        47.54       134.40       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        54.51        23.47       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       64.08        53.19        13.94        48.89       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19T 
        6.44       131.51        61.05        44.05        37.25         8.88 
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-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YX 
      210.08        15.16         7.00        38.27        29.46        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZK 
      202.65        28.08         7.79       357.37        53.52        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       26.56        27.09        50.14        66.67        28.73       174.84 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 
       26.73        77.88         0.20         0.16         9.90       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A8LL 
       84.72        10.13        64.44        32.48        39.58        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41        65.88       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM 
        0.69       212.22        63.02       105.04         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YG-AA3O 
       56.98        52.34         3.75        22.68        10.36        36.03 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        93.07        11.74 

$`AMP PEAK 12(8Q11.21) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       17.03        61.02        16.67       112.04       112.57       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       28.08        31.59        90.90        65.49        23.77       168.00 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ 
       11.87       113.52        42.08        12.10       171.58       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51F 
       46.98        46.32        24.53        13.87         9.34        55.73 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       56.35        22.62        63.81        26.89       125.79       137.92 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL 
       30.84        79.59        11.61        15.19       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       95.24       161.00        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         6.41        18.12        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
       11.11         9.90        48.89        20.38       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-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A180 
       15.68        17.29        52.01         6.35        29.82        94.98 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89        68.15         4.96       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H 
      168.26        13.55        63.35        80.61        13.97        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        2.60        56.84        18.61        56.42        37.35        55.92 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      195.02        17.92        46.82       102.90        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR 
       59.28        67.43        48.72        89.33        54.74        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       55.59        44.88        94.82        21.67        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20       204.66        96.23       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90       248.65        43.23       162.48        71.21        53.26 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
       51.62        13.81       138.81        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       51.35       109.58       148.08        31.40        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        98.40        12.59        13.02        26.37 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG 
      162.08        50.89       148.18        79.99        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P 
       32.05       247.04        33.21         6.77        92.98        15.72 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       34.82        94.39       216.92       228.59        20.91        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       49.48        27.02        77.82        12.43        49.45        22.92 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       47.54        19.30         7.23         2.04        11.74       139.89 
TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-W3-A828 
       62.79        46.36        12.62        50.10       357.04       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
        4.01        42.08       219.16        24.03        38.56        54.38 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT 
       59.41        43.73         2.20        30.18        15.16        23.64 

  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                          0.16                           2.04 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                        369.93                         357.04 
  AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE 
                        54.020                         48.785 
[1] "0.2 - 369.9 (54.0)" "2.0 - 357.0 (48.8)"
[1] "hr=" "1.3"
D12V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 12(8Q11.21) MUTATED                   23             4
  AMP PEAK 12(8Q11.21) WILD-TYPE                 38             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 12(8Q11.21) MUTATED                                          38
  AMP PEAK 12(8Q11.21) WILD-TYPE                                        34
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 12(8Q11.21) MUTATED                    90
  AMP PEAK 12(8Q11.21) WILD-TYPE                 119
D12V4, multiclass
                                           clus
vv                                          AMP PEAK 12(8Q11.21) MUTATED
  DISTANT METASTASIS                                                  23
  PRIMARY TUMOR                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           38
  REGIONAL LYMPH NODE                                                 90
                                           clus
vv                                          AMP PEAK 12(8Q11.21) WILD-TYPE
  DISTANT METASTASIS                                                    38
  PRIMARY TUMOR                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             34
  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
  AMP PEAK 12(8Q11.21) MUTATED             6       1      16        7       10
  AMP PEAK 12(8Q11.21) WILD-TYPE           6       6      12       10       17
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 12(8Q11.21) MUTATED         11         5         6         7
  AMP PEAK 12(8Q11.21) WILD-TYPE       11         9        13         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 12(8Q11.21) MUTATED          23          9         12         24
  AMP PEAK 12(8Q11.21) WILD-TYPE        12          6         20         34
                                vv
clus                             STAGE IV
  AMP PEAK 12(8Q11.21) MUTATED          7
  AMP PEAK 12(8Q11.21) WILD-TYPE       12
D12V5, multiclass
             clus
vv            AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  I OR II NOS                            6                              6
  STAGE 0                                1                              6
  STAGE I                               16                             12
  STAGE IA                               7                             10
  STAGE IB                              10                             17
  STAGE II                              11                             11
  STAGE IIA                              5                              9
  STAGE IIB                              6                             13
  STAGE IIC                              7                              5
  STAGE III                             23                             12
  STAGE IIIA                             9                              6
  STAGE IIIB                            12                             20
  STAGE IIIC                            24                             34
  STAGE IV                               7                             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 12(8Q11.21) MUTATED      34 36 28 29
  AMP PEAK 12(8Q11.21) WILD-TYPE    29 35 46 38
D12V6, multiclass
       clus
vv      AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  T0+T1                           34                             29
  T2                              36                             35
  T3                              28                             46
  T4                              29                             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
  AMP PEAK 12(8Q11.21) MUTATED   71 33 17 19
  AMP PEAK 12(8Q11.21) WILD-TYPE 97 28 21 28
D12V7, multiclass
    clus
vv   AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  N0                           71                             97
  N1                           33                             28
  N2                           17                             21
  N3                           19                             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 12(8Q11.21) MUTATED   140   2   1   1   3
  AMP PEAK 12(8Q11.21) WILD-TYPE 166   2   2   3   6
D12V8, multiclass
     clus
vv    AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  M0                           140                            166
  M1                             2                              2
  M1A                            1                              2
  M1B                            1                              3
  M1C                            3                              6
[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   52 36
  AMP PEAK 12(8Q11.21) WILD-TYPE 77 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q11.21) MUTATED     52   36
  AMP PEAK 12(8Q11.21) WILD-TYPE   77   51
     clus
vv    AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  NO                            52                             77
  YES                           36                             51
[1] 2 2
[1] FALSE
D12V10, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q11.21) MUTATED    24 132
  AMP PEAK 12(8Q11.21) WILD-TYPE  19 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q11.21) MUTATED     24  132
  AMP PEAK 12(8Q11.21) WILD-TYPE   19  172
     clus
vv    AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  NO                            24                             19
  YES                          132                            172
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q11.21) MUTATED    58  98
  AMP PEAK 12(8Q11.21) WILD-TYPE  73 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q11.21) MUTATED     58   98
  AMP PEAK 12(8Q11.21) WILD-TYPE   73  119
        clus
vv       AMP PEAK 12(8Q11.21) MUTATED AMP PEAK 12(8Q11.21) WILD-TYPE
  FEMALE                           58                             73
  MALE                             98                            119
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q11.21) MUTATED       5                         0   142
  AMP PEAK 12(8Q11.21) WILD-TYPE     0                         1   184
D12V13, multiclass
                           clus
vv                          AMP PEAK 12(8Q11.21) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              142
                           clus
vv                          AMP PEAK 12(8Q11.21) WILD-TYPE
  ASIAN                                                  0
  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"
D12V14, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q11.21) MUTATED     4 149
  AMP PEAK 12(8Q11.21) WILD-TYPE   3 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q11.21) MUTATED      4  149
  AMP PEAK 12(8Q11.21) WILD-TYPE    3  185
                        clus
vv                       AMP PEAK 12(8Q11.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       AMP PEAK 12(8Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            185
[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   89 87
  AMP PEAK 13(8Q24.21) WILD-TYPE 79 78
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           176                            157 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                            87                             78 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
        6.97         6.97        16.47       111.09        70.16        22.55 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       81.24        10.29        85.32        88.50        86.76        44.19 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       56.19        64.44        59.57        15.25        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       13.32         6.31         9.34       103.59        26.37        29.23 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR 
       93.21        54.31        32.28        21.44        52.01        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D9-A6EA 
       17.72        23.11         4.18       142.45        87.62        11.31 
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-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       13.68         9.99         7.00        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        23.15        19.00         0.20        10.55         6.31 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        1.12        60.23        37.97        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A5 
        1.08         8.84         9.99        30.44         2.43         9.67 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       17.98        60.00        47.21        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.69         5.42        13.02        98.27         2.70         6.18 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
        2.73         7.96        63.42        25.08        26.99        60.49 
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-A19T TCGA-ER-A2NC TCGA-ER-A2ND 
       42.84         9.57        36.07         6.58        11.80         1.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A729 
       13.08         9.04         6.58        22.49        85.74         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX 
        3.58         5.36        13.28         4.70        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       11.01        23.80        15.52         7.33        20.38         8.22 
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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       40.64         8.68         0.82         3.22         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT 
       14.20         5.98         2.27         0.20         0.16         9.90 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LL 
       10.13        16.24        12.16        14.70        11.84        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       14.50        15.81        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA21 
        0.69       164.19         8.98        60.03        10.98        71.01 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
        3.42        21.83        19.96         1.94         6.18         4.70 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        3.02         8.52        32.42       110.79        28.08        45.83 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
        8.38        21.14        68.22        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF 
        6.31        92.42       114.67        46.98        46.32        24.00 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       54.74        31.30        32.61        25.78       110.24        47.87 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL 
       29.72        22.06        10.22        15.19       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
       75.65       124.47        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 
       21.93         5.72         9.90        48.79        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
       25.15         4.93        22.36         6.64        19.36        14.83 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       13.35        13.22        11.57         8.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        7.99         9.90        11.15        39.62         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.09        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       36.33        51.12        34.29        30.08        19.43        16.01 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
        1.15        34.98        36.33         8.84        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       29.46        44.25        14.56       125.65       111.91        56.02 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF 
       21.60        53.16        52.67         5.56        51.62        13.81 
TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       12.72        16.14         0.95        27.35        18.41        21.73 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       33.60        31.40        18.61         5.72        76.41        25.18 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 
        3.52        11.90        11.11        34.68        17.72        78.44 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        1.51        12.62        11.74         1.71         5.62        18.41 
TCGA-FR-A69P TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       15.72         2.20         3.29        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-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       17.33         7.23         0.85        11.61        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-W3-AA1O 
       84.72        15.42        10.65        14.50         0.43         2.99 
TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA4 
      185.16        11.84         5.49         5.36         1.08        12.07 
TCGA-Z2-A8RT 
        8.22 

  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          0.13                           0.13 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        164.19                         185.16 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                         14.50                          15.42 
[1] "0.1 - 164.2 (14.5)" "0.1 - 185.2 (15.4)"
[1] "hr=" "1"  
D13V2, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(8Q24.21) MUTATED   90 87
  AMP PEAK 13(8Q24.21) WILD-TYPE 83 79
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           177                            162 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                            87                             79 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
       61.02        12.99        16.57       112.04        71.80        31.59 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       95.74        43.43       103.10       115.53        86.76        62.07 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       56.19        66.08        59.57        58.06       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR 
      174.84       145.12        32.94        22.62       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D9-A1JW 
       18.18       125.19        58.52       228.99       137.79         3.65 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        66.25        22.95        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
      194.83       176.55        35.93        10.49       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y 
       10.16        17.85        68.25        54.02        12.20        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        8.65        33.73       133.81        47.84        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       64.64         2.60        14.47        55.92       369.93        25.87 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM 
       39.29       314.56       161.03       208.04        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       90.97       126.81        13.91        55.59       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP 
       19.76       268.73        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 
      134.40       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-A19T TCGA-ER-A2NC 
       61.05        44.05        50.89        37.25         8.88        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       23.34        16.37       247.04        80.32        46.98       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW 
      210.08        15.16         7.00        38.27        29.46       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC 
       48.59       228.59       202.65        28.08         7.79       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 
      148.80        53.16        26.56        27.09        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
       28.73       174.84        26.73        77.88         0.20         0.16 
TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
        9.90        10.13        64.44        32.48        39.58        46.36 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       21.37        59.41        65.88       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
        0.33         0.69       212.22        63.02       121.08        42.08 
TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        54.38         8.61        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
       52.34         3.75        22.68        30.18        10.36        36.03 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        93.07        11.74 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       17.03        16.67       112.57       133.25        28.08        90.90 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       65.49        23.77       168.00        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF 
       12.10       171.58       130.72        46.98        46.32        24.53 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       55.73        56.35        63.81        26.89       125.79       137.92 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL 
       30.84        79.59        11.61        15.19       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       95.24       161.00        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         6.41        18.12        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
        9.90        48.89       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EB-A5UN 
       23.44        68.09        28.60        15.68        17.29        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        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       80.61        13.97        56.84        18.61        56.42        37.35 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      195.02        17.92        46.82       102.90        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR 
       59.28        67.43        48.72        89.33        54.74        14.30 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       44.88        94.82        21.67        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ 
      103.20       204.66       158.63       203.05       167.90        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH 
      162.48        71.21        53.26        51.62        13.81       138.81 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32       201.80        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       31.40        35.44         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
       13.02        26.37       162.08       148.18        79.99        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P 
       31.27        32.05        33.21         6.77        92.98        15.72 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE 
       34.82        94.39        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        19.30 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-W3-AA1O TCGA-W3-AA1W 
       62.79        12.62        50.10       357.04         4.01       219.16 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-Z2-A8RT 
       24.03        38.56        43.73         2.20        15.16        23.64 

  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          0.16                           2.04 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        369.93                         357.04 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                         53.52                          48.13 
[1] "0.2 - 369.9 (53.5)" "2.0 - 357.0 (48.1)"
[1] "hr=" "1.2"
D13V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 13(8Q24.21) MUTATED                   27             4
  AMP PEAK 13(8Q24.21) WILD-TYPE                 34             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 13(8Q24.21) MUTATED                                          43
  AMP PEAK 13(8Q24.21) WILD-TYPE                                        29
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 13(8Q24.21) MUTATED                   106
  AMP PEAK 13(8Q24.21) WILD-TYPE                 103
D13V4, multiclass
                                           clus
vv                                          AMP PEAK 13(8Q24.21) MUTATED
  DISTANT METASTASIS                                                  27
  PRIMARY TUMOR                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           43
  REGIONAL LYMPH NODE                                                106
                                           clus
vv                                          AMP PEAK 13(8Q24.21) WILD-TYPE
  DISTANT METASTASIS                                                    34
  PRIMARY TUMOR                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             29
  REGIONAL LYMPH NODE                                                  103
[1] 4 2
[1] 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             6       1      17        9       12
  AMP PEAK 13(8Q24.21) WILD-TYPE           6       6      11        8       15
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 13(8Q24.21) MUTATED         13         8         6         7
  AMP PEAK 13(8Q24.21) WILD-TYPE        9         6        13         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 13(8Q24.21) MUTATED          25         10         16         26
  AMP PEAK 13(8Q24.21) WILD-TYPE        10          5         16         32
                                vv
clus                             STAGE IV
  AMP PEAK 13(8Q24.21) MUTATED         10
  AMP PEAK 13(8Q24.21) WILD-TYPE        9
D13V5, multiclass
             clus
vv            AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  I OR II NOS                            6                              6
  STAGE 0                                1                              6
  STAGE I                               17                             11
  STAGE IA                               9                              8
  STAGE IB                              12                             15
  STAGE II                              13                              9
  STAGE IIA                              8                              6
  STAGE IIB                              6                             13
  STAGE IIC                              7                              5
  STAGE III                             25                             10
  STAGE IIIA                            10                              5
  STAGE IIIB                            16                             16
  STAGE IIIC                            26                             32
  STAGE IV                              10                              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 13(8Q24.21) MUTATED      40 41 35 33
  AMP PEAK 13(8Q24.21) WILD-TYPE    23 30 39 34
D13V6, multiclass
       clus
vv      AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  T0+T1                           40                             23
  T2                              41                             30
  T3                              35                             39
  T4                              33                             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 13(8Q24.21) MUTATED   82 36 22 23
  AMP PEAK 13(8Q24.21) WILD-TYPE 86 25 16 24
D13V7, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  N0                           82                             86
  N1                           36                             25
  N2                           22                             16
  N3                           23                             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 13(8Q24.21) MUTATED   162   2   2   1   5
  AMP PEAK 13(8Q24.21) WILD-TYPE 144   2   1   3   4
D13V8, multiclass
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  M0                           162                            144
  M1                             2                              2
  M1A                            2                              1
  M1B                            1                              3
  M1C                            5                              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"
D13V9, binary
                                cls
clus                              0  1
  AMP PEAK 13(8Q24.21) MUTATED   64 42
  AMP PEAK 13(8Q24.21) WILD-TYPE 65 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     64   42
  AMP PEAK 13(8Q24.21) WILD-TYPE   65   45
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                            64                             65
  YES                           42                             45
[1] 2 2
[1] FALSE
D13V10, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED    25 156
  AMP PEAK 13(8Q24.21) WILD-TYPE  18 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     25  156
  AMP PEAK 13(8Q24.21) WILD-TYPE   18  148
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                            25                             18
  YES                          156                            148
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED    66 115
  AMP PEAK 13(8Q24.21) WILD-TYPE  65 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     66  115
  AMP PEAK 13(8Q24.21) WILD-TYPE   65  102
        clus
vv       AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  FEMALE                           66                             65
  MALE                            115                            102
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8Q24.21) MUTATED       5                         0   165
  AMP PEAK 13(8Q24.21) WILD-TYPE     0                         1   161
D13V13, multiclass
                           clus
vv                          AMP PEAK 13(8Q24.21) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              165
                           clus
vv                          AMP PEAK 13(8Q24.21) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                161
[1] 3 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     4 174
  AMP PEAK 13(8Q24.21) WILD-TYPE   3 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      4  174
  AMP PEAK 13(8Q24.21) WILD-TYPE    3  160
                        clus
vv                       AMP PEAK 13(8Q24.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          174
                        clus
vv                       AMP PEAK 13(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            160
[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    32  31
  AMP PEAK 14(11Q13.3) WILD-TYPE 136 134
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            63                            270 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            31                            134 
$`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        86.76        44.19        59.57 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A8GB TCGA-D9-A3Z3 
       82.29        13.32        24.00        93.21        29.72        21.93 
TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A180 
       13.22         7.00        13.15        19.00         0.20         8.12 
TCGA-EE-A20F TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GP 
       15.85        32.15         8.09        51.12        47.21         5.42 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MM TCGA-EE-A3JA TCGA-EE-A3JB 
        1.15         8.84        47.51        56.02        22.22         0.95 
TCGA-EE-A3JI TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       33.60        28.60        42.84         9.57         6.58        17.72 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A729 TCGA-FS-A1YW 
       13.08         9.04         6.58         5.62         6.71        64.47 
TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        3.45         3.39         8.22        12.89         8.65        49.15 
TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A268 
       40.64         3.22         2.27         7.23        10.13        15.42 
TCGA-GN-A26D TCGA-GN-A8LL TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       14.70        14.50         5.49         7.10        21.07         3.72 
TCGA-WE-A8ZX TCGA-YG-AA3P TCGA-Z2-AA3V 
       21.83         4.70         5.98 

$`AMP PEAK 14(11Q13.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       32.42        70.16       110.79        28.08        45.83        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-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       36.16         6.31        92.42        56.19        64.44       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO 
       15.25        46.98        46.32        61.38         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        26.37        29.23        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.28        21.44        32.61        25.78       110.24        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       47.87        13.68        17.72        23.11        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      124.47        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        5.72         9.90        11.31        14.60        48.79        35.80 
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-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-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL 
       17.56        14.83         0.20         0.13        23.15        13.35 
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        60.23         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        30.44         2.43        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       60.00        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        55.69        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        2.70         6.18         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
        7.96        14.56        63.42       125.65       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       16.14        27.35        18.41        21.73        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
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-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       13.45        34.68        36.07        78.44        11.80         1.87 
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-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       85.74        15.72         3.58         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.70         3.29        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.33         7.30        20.38        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZU 
       30.87        12.92        47.38        52.08         8.81         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       14.20        10.78         5.98         6.41         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.13         0.16        17.33         9.90         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 
       44.28        31.33        84.72        16.24        12.16        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       10.65        14.50        14.50        15.81         0.43        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        5.79        18.05         0.33         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       60.03         2.99        10.98       185.16        71.01        11.84 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
        6.48        18.67        13.12         3.42         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.96         1.94        12.07         6.18         8.22         6.67 

  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                          0.20                           0.13 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                         93.21                         185.16 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                        13.220                         15.385 
[1] "0.2 - 93.2 (13.2)"  "0.1 - 185.2 (15.4)"
[1] "hr=" "1.1"
D14V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(11Q13.3) MUTATED    32  31
  AMP PEAK 14(11Q13.3) WILD-TYPE 141 135
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            63                            276 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                            31                            135 
$`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        86.76        62.07        59.57 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A8GB TCGA-D9-A3Z3 
      166.52        60.23        24.53       174.84        30.84        22.29 
TCGA-D9-A6EC TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A180 
       66.25        10.49        13.87        54.02        12.20        94.98 
TCGA-EE-A20F TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GP 
       91.56       195.02        17.92        59.28       208.04        13.91 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MM TCGA-EE-A3JA TCGA-EE-A3JB 
       14.30        21.67        61.51       167.90        53.19       201.80 
TCGA-EE-A3JI TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
      148.08        61.05        44.05        50.89         8.88       148.18 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A729 TCGA-FS-A1YW 
       16.37       247.04        80.32         6.77       210.08       216.92 
TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       48.59        48.85        53.52        23.93       133.55       148.80 
TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A268 
       53.16        50.14        77.88         7.23        10.13        62.79 
TCGA-GN-A26D TCGA-GN-A8LL TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       39.58        21.37        38.56         8.61        56.98        52.34 
TCGA-WE-A8ZX TCGA-YG-AA3P TCGA-Z2-AA3V 
       22.68        14.43        11.74 

$`AMP PEAK 14(11Q13.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        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-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       42.08        12.10       171.58        56.19        66.08       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO 
       58.06        46.98        46.32        86.93        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75        45.30        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      137.92       178.32        18.18       125.19        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       137.79        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       54.67         3.65         6.41        18.12        11.34        11.11 
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        68.25        17.29        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       133.81       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       369.93        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        36.82        39.29        86.14        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      161.03        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       126.81        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       28.83        19.76        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       34.32        27.35        51.35       109.58        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-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-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      131.51       162.08        37.25        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       20.15        31.27        32.05        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      174.21        15.72        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       29.46        94.39       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.79        27.72       357.37        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZU 
       32.75        47.38       101.26        74.73        11.41        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       47.54         0.16        19.30         9.90         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 
      139.89       117.93        84.72        64.44        32.48        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       12.62        50.10        59.41        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        6.67        18.05         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      121.08         4.01        42.08       219.16       105.04        24.03 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       54.38        90.28        59.41         3.75        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       30.18        10.36        15.16        36.03        23.64        93.07 

  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                          6.77                           0.16 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                        247.04                         369.93 
  AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE 
                         53.16                          49.17 
[1] "6.8 - 247.0 (53.2)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1"  
D14V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 14(11Q13.3) MUTATED                    9             3
  AMP PEAK 14(11Q13.3) WILD-TYPE                 52             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 14(11Q13.3) MUTATED                                          11
  AMP PEAK 14(11Q13.3) WILD-TYPE                                        61
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 14(11Q13.3) MUTATED                    43
  AMP PEAK 14(11Q13.3) WILD-TYPE                 166
D14V4, multiclass
                                           clus
vv                                          AMP PEAK 14(11Q13.3) MUTATED
  DISTANT METASTASIS                                                   9
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           11
  REGIONAL LYMPH NODE                                                 43
                                           clus
vv                                          AMP PEAK 14(11Q13.3) WILD-TYPE
  DISTANT METASTASIS                                                    52
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             61
  REGIONAL LYMPH NODE                                                  166
[1] 4 2
[1] 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       9        2        4
  AMP PEAK 14(11Q13.3) WILD-TYPE           6       5      19       15       23
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 14(11Q13.3) MUTATED          3         2         4         3
  AMP PEAK 14(11Q13.3) WILD-TYPE       19        12        15         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 14(11Q13.3) MUTATED           6          2          8          9
  AMP PEAK 14(11Q13.3) WILD-TYPE        29         13         24         49
                                vv
clus                             STAGE IV
  AMP PEAK 14(11Q13.3) MUTATED          1
  AMP PEAK 14(11Q13.3) WILD-TYPE       18
D14V5, multiclass
             clus
vv            AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  I OR II NOS                            6                              6
  STAGE 0                                2                              5
  STAGE I                                9                             19
  STAGE IA                               2                             15
  STAGE IB                               4                             23
  STAGE II                               3                             19
  STAGE IIA                              2                             12
  STAGE IIB                              4                             15
  STAGE IIC                              3                              9
  STAGE III                              6                             29
  STAGE IIIA                             2                             13
  STAGE IIIB                             8                             24
  STAGE IIIC                             9                             49
  STAGE IV                               1                             18
[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      10 17  9 16
  AMP PEAK 14(11Q13.3) WILD-TYPE    53 54 65 51
D14V6, multiclass
       clus
vv      AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  T0+T1                           10                             53
  T2                              17                             54
  T3                               9                             65
  T4                              16                             51
[1] 4 2
[1] 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    36  11   3  10
  AMP PEAK 14(11Q13.3) WILD-TYPE 132  50  35  37
D14V7, multiclass
    clus
vv   AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  N0                           36                            132
  N1                           11                             50
  N2                            3                             35
  N3                           10                             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                              M0  M1 M1A M1B M1C
  AMP PEAK 14(11Q13.3) MUTATED    60   0   1   0   0
  AMP PEAK 14(11Q13.3) WILD-TYPE 246   4   2   4   9
D14V8, multiclass
     clus
vv    AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  M0                            60                            246
  M1                             0                              4
  M1A                            1                              2
  M1B                            0                              4
  M1C                            0                              9
[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    23  15
  AMP PEAK 14(11Q13.3) WILD-TYPE 106  72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED     23   15
  AMP PEAK 14(11Q13.3) WILD-TYPE  106   72
     clus
vv    AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  NO                            23                            106
  YES                           15                             72
[1] 2 2
[1] FALSE
D14V10, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q13.3) MUTATED     8  57
  AMP PEAK 14(11Q13.3) WILD-TYPE  35 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      8   57
  AMP PEAK 14(11Q13.3) WILD-TYPE   35  247
     clus
vv    AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  NO                             8                             35
  YES                           57                            247
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, binary
                                cls
clus                               0   1
  AMP PEAK 14(11Q13.3) MUTATED    27  39
  AMP PEAK 14(11Q13.3) WILD-TYPE 104 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED     27   39
  AMP PEAK 14(11Q13.3) WILD-TYPE  104  178
        clus
vv       AMP PEAK 14(11Q13.3) MUTATED AMP PEAK 14(11Q13.3) WILD-TYPE
  FEMALE                           27                            104
  MALE                             39                            178
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(11Q13.3) MUTATED       2                         1    59
  AMP PEAK 14(11Q13.3) WILD-TYPE     3                         0   267
D14V13, multiclass
                           clus
vv                          AMP PEAK 14(11Q13.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               59
                           clus
vv                          AMP PEAK 14(11Q13.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                267
[1] 3 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     1  65
  AMP PEAK 14(11Q13.3) WILD-TYPE   6 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(11Q13.3) MUTATED      1   65
  AMP PEAK 14(11Q13.3) WILD-TYPE    6  269
                        clus
vv                       AMP PEAK 14(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       AMP PEAK 14(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            269
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(12Q14.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(12Q14.1) MUTATED    24  29
  AMP PEAK 15(12Q14.1) WILD-TYPE 144 136
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                            53                            280 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                            29                            136 
$`AMP PEAK 15(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        29.23        52.01 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 
       17.72        23.11         9.90        48.79        35.80        17.56 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A29D 
       13.15        13.35        10.55         6.31         8.12        11.15 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-EE-A3J5 
       36.33        51.12        47.21         8.84        53.16        21.60 
TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A2NE 
       18.41        12.95        25.18         3.78        28.60         1.51 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZK 
        6.58         1.71         6.71        19.53        11.08        12.89 
TCGA-FS-A1ZM TCGA-FS-A4F5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       47.38        28.73        31.33        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1V TCGA-YG-AA3O 
       14.70        18.05         8.98        10.98         6.18 

$`AMP PEAK 15(12Q14.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      110.79        28.08        45.83        81.24        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        86.76        11.41        44.19 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C7 
        7.50        36.16         6.31        92.42        59.57        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        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78       110.24        47.87        13.68 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       29.72        22.06        10.22        15.19         4.18       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      108.79        38.93        75.65       124.47        87.62        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
        5.56        24.07         4.01        21.93         5.72        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 
       23.15        19.00        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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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 
       62.79         8.55        36.85         1.08        39.62         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        30.44         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        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       125.65       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        60.49        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        0.95        27.35        21.73        33.60        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       38.40         5.72        76.41         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
      114.15        34.88         4.21        13.45        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
        1.87        13.08        12.62        11.74         9.04        22.49 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
        5.62        18.41        85.74        15.72         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       13.28         2.20         4.70         3.29        64.47         3.45 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        3.39        20.38         8.22         7.17        30.87        12.92 
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-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 
        0.85        11.61        44.28        84.72        10.13        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       10.65        14.50        14.50        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
       11.05         5.79         0.33         0.69       164.19        60.03 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
        2.99       185.16        71.01        11.84         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        7.10        18.67        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       21.83         5.36         1.08        19.96         1.94        12.07 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                          1.51                           0.13 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                        114.67                         185.16 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                         17.56                          14.37 
[1] "1.5 - 114.7 (17.6)" "0.1 - 185.2 (14.4)"
[1] "hr=" "1.1"
D15V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(12Q14.1) MUTATED    24  29
  AMP PEAK 15(12Q14.1) WILD-TYPE 149 137
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                            53                            286 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                            29                            137 
$`AMP PEAK 15(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        45.30       135.75 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 
       18.18       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        17.29        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 
       86.14        59.28       208.04        21.67       162.48        36.95 
TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A2NE 
       51.35        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 TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1V TCGA-YG-AA3O 
       39.58        18.05        63.02        42.08        36.03 

$`AMP PEAK 15(12Q14.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        86.76        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C7 
      113.52        42.08        12.10       171.58        59.57        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       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       125.79       137.92       178.32 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       30.84        79.59        11.61        15.19        58.52       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      170.20        89.13        95.24       161.00       137.79        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         6.41 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
       18.12        11.34        22.29        11.11        25.18        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-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-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       28.60        10.49        15.68        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A181 
       54.02        52.01         6.35        12.20        29.82        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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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 
       63.78        72.07        64.64         2.60        56.84        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       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       161.03        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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       134.40        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35       109.58       148.08        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       50.76         9.17        77.75        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
      268.93       152.35         6.44       131.51        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
        6.77        92.98       174.21        15.72        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        29.46        94.39       216.92        48.59 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85       357.37        53.52         9.70        32.75        47.38 
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-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 
        2.04        11.74       139.89        84.72        10.13        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       12.62        50.10        21.37        59.41        65.88       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
      294.77         6.67         0.33         0.69       212.22       121.08 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
        4.01       219.16       105.04        24.03        38.56        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.61        90.28        56.98        59.41        52.34         3.75 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       22.68        43.73         2.20        30.18        10.36        15.16 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                          8.65                           0.16 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                        215.44                         369.93 
  AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE 
                        45.300                         51.255 
[1] "8.7 - 215.4 (45.3)" "0.2 - 369.9 (51.3)"
[1] "hr=" "1.3"
D15V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 15(12Q14.1) MUTATED                    6             1
  AMP PEAK 15(12Q14.1) WILD-TYPE                 55             4
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 15(12Q14.1) MUTATED                                          13
  AMP PEAK 15(12Q14.1) WILD-TYPE                                        59
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 15(12Q14.1) MUTATED                    33
  AMP PEAK 15(12Q14.1) WILD-TYPE                 176
D15V4, multiclass
                                           clus
vv                                          AMP PEAK 15(12Q14.1) MUTATED
  DISTANT METASTASIS                                                   6
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           13
  REGIONAL LYMPH NODE                                                 33
                                           clus
vv                                          AMP PEAK 15(12Q14.1) WILD-TYPE
  DISTANT METASTASIS                                                    55
  PRIMARY TUMOR                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             59
  REGIONAL LYMPH NODE                                                  176
[1] 4 2
[1] 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(12Q14.1) MUTATED             1       1       5        1        4
  AMP PEAK 15(12Q14.1) WILD-TYPE          11       6      23       16       23
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 15(12Q14.1) MUTATED          4         0         4         4
  AMP PEAK 15(12Q14.1) WILD-TYPE       18        14        15         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 15(12Q14.1) MUTATED           6          4          8          7
  AMP PEAK 15(12Q14.1) WILD-TYPE        29         11         24         51
                                vv
clus                             STAGE IV
  AMP PEAK 15(12Q14.1) MUTATED          2
  AMP PEAK 15(12Q14.1) WILD-TYPE       17
D15V5, multiclass
             clus
vv            AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  I OR II NOS                            1                             11
  STAGE 0                                1                              6
  STAGE I                                5                             23
  STAGE IA                               1                             16
  STAGE IB                               4                             23
  STAGE II                               4                             18
  STAGE IIA                              0                             14
  STAGE IIB                              4                             15
  STAGE IIC                              4                              8
  STAGE III                              6                             29
  STAGE IIIA                             4                             11
  STAGE IIIB                             8                             24
  STAGE IIIC                             7                             51
  STAGE IV                               2                             17
[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(12Q14.1) MUTATED      10  9 11 15
  AMP PEAK 15(12Q14.1) WILD-TYPE    53 62 63 52
D15V6, multiclass
       clus
vv      AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  T0+T1                           10                             53
  T2                               9                             62
  T3                              11                             63
  T4                              15                             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
  AMP PEAK 15(12Q14.1) MUTATED    26  15   4   6
  AMP PEAK 15(12Q14.1) WILD-TYPE 142  46  34  41
D15V7, multiclass
    clus
vv   AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  N0                           26                            142
  N1                           15                             46
  N2                            4                             34
  N3                            6                             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                              M0  M1 M1A M1B M1C
  AMP PEAK 15(12Q14.1) MUTATED    49   0   1   0   1
  AMP PEAK 15(12Q14.1) WILD-TYPE 257   4   2   4   8
D15V8, multiclass
     clus
vv    AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  M0                            49                            257
  M1                             0                              4
  M1A                            1                              2
  M1B                            0                              4
  M1C                            1                              8
[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(12Q14.1) MUTATED    22  16
  AMP PEAK 15(12Q14.1) WILD-TYPE 107  71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED     22   16
  AMP PEAK 15(12Q14.1) WILD-TYPE  107   71
     clus
vv    AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  NO                            22                            107
  YES                           16                             71
[1] 2 2
[1] FALSE
D15V10, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED     3  51
  AMP PEAK 15(12Q14.1) WILD-TYPE  40 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED      3   51
  AMP PEAK 15(12Q14.1) WILD-TYPE   40  253
     clus
vv    AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  NO                             3                             40
  YES                           51                            253
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, binary
                                cls
clus                               0   1
  AMP PEAK 15(12Q14.1) MUTATED    21  33
  AMP PEAK 15(12Q14.1) WILD-TYPE 110 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED     21   33
  AMP PEAK 15(12Q14.1) WILD-TYPE  110  184
        clus
vv       AMP PEAK 15(12Q14.1) MUTATED AMP PEAK 15(12Q14.1) WILD-TYPE
  FEMALE                           21                            110
  MALE                             33                            184
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(12Q14.1) MUTATED       2                         0    51
  AMP PEAK 15(12Q14.1) WILD-TYPE     3                         1   275
D15V13, multiclass
                           clus
vv                          AMP PEAK 15(12Q14.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               51
                           clus
vv                          AMP PEAK 15(12Q14.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                275
[1] 3 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(12Q14.1) MUTATED     2  51
  AMP PEAK 15(12Q14.1) WILD-TYPE   5 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(12Q14.1) MUTATED      2   51
  AMP PEAK 15(12Q14.1) WILD-TYPE    5  283
                        clus
vv                       AMP PEAK 15(12Q14.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           51
                        clus
vv                       AMP PEAK 15(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            283
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(12Q15) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 16(12Q15) MUTATED    24  28
  AMP PEAK 16(12Q15) WILD-TYPE 144 137
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          52                          281 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          28                          137 
$`AMP PEAK 16(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        29.23        31.30       110.24 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       52.01        17.72        23.11        13.22        48.79        35.80 
TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
       17.56        13.35        10.55         8.12        11.15        36.33 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-EE-A3J5 TCGA-EE-A3JE 
       51.12        47.21         8.84        53.16        21.60        18.41 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       33.60        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 TCGA-GN-A8LK TCGA-QB-AA9O 
       16.24        15.42        12.16        14.70        14.50        18.05 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8ZY TCGA-YG-AA3O 
        8.98        10.98         5.36         6.18 

$`AMP PEAK 16(12Q15) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
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-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       44.19         7.50        36.16         6.31        92.42        59.57 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32        82.29        13.32         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
      103.59        26.37        93.21        54.74        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GB 
       21.44        32.61        25.78        47.87        13.68        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       22.06        10.22        15.19         4.18       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       38.93        75.65       124.47        87.62        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       24.07         4.01        21.93         5.72         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 
       23.15        19.00        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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        62.79         8.55        36.85         1.08        39.62 
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        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
        9.67        34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        21.60        60.49        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.95        27.35        21.73        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       38.40         5.72        76.41         3.52        11.90        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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       13.08        12.62        11.74         9.04        22.49         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        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-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-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.17        30.87        12.92        52.08         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        3.22         7.36        14.20        10.78         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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       84.72        10.13        11.84        10.65        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.81         0.43        11.05         5.79         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      164.19        60.03         2.99       185.16        71.01        11.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        5.49         6.48         7.10        18.67        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        3.72         3.42        21.83         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         4.70         8.22         6.67         5.98 

  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                        1.51                         0.13 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                      114.67                       185.16 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                       18.23                        13.68 
[1] "1.5 - 114.7 (18.2)" "0.1 - 185.2 (13.7)"
[1] "hr=" "1.1"
D16V2, survival
                              sevent
clus2                            0   1
  AMP PEAK 16(12Q15) MUTATED    25  28
  AMP PEAK 16(12Q15) WILD-TYPE 148 138
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          53                          286 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          28                          138 
$`AMP PEAK 16(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        45.30        56.35       125.79 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1X3 TCGA-D9-A6EC TCGA-DA-A1HV 
      135.75        18.18       125.19        18.12        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D 
       36.03       215.44        17.29        27.22        94.98        13.97 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-EE-A3J5 
       86.14        59.28       208.04        21.67       162.48        36.95 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G 
       51.35       148.08        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 TCGA-GN-A8LK 
       28.73        64.44        62.79        32.48        39.58        50.10 
TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8ZY TCGA-YG-AA3O 
       18.05        63.02        42.08        43.73        36.03 

$`AMP PEAK 16(12Q15) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
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-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       62.07       113.52        42.08        12.10       171.58        59.57 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32       166.52        60.23        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
      103.59        39.75       174.84        55.73       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GB 
       22.62        63.81        26.89       137.92       178.32        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        11.61        15.19        58.52       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13        95.24       161.00       137.79        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      117.17       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY 
       22.29        11.11         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        68.25        54.02 
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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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 
       63.78        72.07        64.64         2.60        56.84        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       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       161.03        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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       134.40        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
      201.80        27.35       109.58        31.40        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19J 
        9.17        77.75        12.59        13.02        26.37         6.44 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
        8.88       148.18        79.99        43.82        23.34        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       31.27        32.05       247.04        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        29.46        94.39       216.92        48.59 
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-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       32.75        47.38        74.73        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67       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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       10.13        46.36        12.62        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      357.04       294.77         6.67         0.33         0.69       212.22 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
      121.08         4.01       219.16       105.04        24.03        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       54.38         8.61        90.28        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.75        22.68         2.20        30.18        10.36        15.16 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                       13.94                         0.16 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                      268.93                       369.93 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                      56.190                       49.465 
[1] "13.9 - 268.9 (56.2)" "0.2 - 369.9 (49.5)" 
[1] "hr=" "1.1"
D16V3, continuous
                              vv
clus                           DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 16(12Q15) MUTATED                    7             1
  AMP PEAK 16(12Q15) WILD-TYPE                 54             4
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 16(12Q15) MUTATED                                          15
  AMP PEAK 16(12Q15) WILD-TYPE                                        57
                              vv
clus                           REGIONAL LYMPH NODE
  AMP PEAK 16(12Q15) MUTATED                    31
  AMP PEAK 16(12Q15) WILD-TYPE                 178
D16V4, multiclass
                                           clus
vv                                          AMP PEAK 16(12Q15) MUTATED
  DISTANT METASTASIS                                                 7
  PRIMARY TUMOR                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                         15
  REGIONAL LYMPH NODE                                               31
                                           clus
vv                                          AMP PEAK 16(12Q15) WILD-TYPE
  DISTANT METASTASIS                                                  54
  PRIMARY TUMOR                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           57
  REGIONAL LYMPH NODE                                                178
[1] 4 2
[1] 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(12Q15) MUTATED             2       1       5        1        5
  AMP PEAK 16(12Q15) WILD-TYPE          10       6      23       16       22
                              vv
clus                           STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 16(12Q15) MUTATED          4         1         2         2         6
  AMP PEAK 16(12Q15) WILD-TYPE       18        13        17        10        29
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 16(12Q15) MUTATED            4          8          7        2
  AMP PEAK 16(12Q15) WILD-TYPE         11         24         51       17
D16V5, multiclass
             clus
vv            AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  I OR II NOS                          2                           10
  STAGE 0                              1                            6
  STAGE I                              5                           23
  STAGE IA                             1                           16
  STAGE IB                             5                           22
  STAGE II                             4                           18
  STAGE IIA                            1                           13
  STAGE IIB                            2                           17
  STAGE IIC                            2                           10
  STAGE III                            6                           29
  STAGE IIIA                           4                           11
  STAGE IIIB                           8                           24
  STAGE IIIC                           7                           51
  STAGE IV                             2                           17
[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(12Q15) MUTATED      11 10 10 13
  AMP PEAK 16(12Q15) WILD-TYPE    52 61 64 54
D16V6, multiclass
       clus
vv      AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  T0+T1                         11                           52
  T2                            10                           61
  T3                            10                           64
  T4                            13                           54
[1] 4 2
[1] 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(12Q15) MUTATED    24  15   5   6
  AMP PEAK 16(12Q15) WILD-TYPE 144  46  33  41
D16V7, multiclass
    clus
vv   AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  N0                         24                          144
  N1                         15                           46
  N2                          5                           33
  N3                          6                           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                            M0  M1 M1A M1B M1C
  AMP PEAK 16(12Q15) MUTATED    49   0   0   0   2
  AMP PEAK 16(12Q15) WILD-TYPE 257   4   3   4   7
D16V8, multiclass
     clus
vv    AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  M0                          49                          257
  M1                           0                            4
  M1A                          0                            3
  M1B                          0                            4
  M1C                          2                            7
[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(12Q15) MUTATED    23  13
  AMP PEAK 16(12Q15) WILD-TYPE 106  74
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED     23   13
  AMP PEAK 16(12Q15) WILD-TYPE  106   74
     clus
vv    AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  NO                          23                          106
  YES                         13                           74
[1] 2 2
[1] FALSE
D16V10, binary
                              cls
clus                             0   1
  AMP PEAK 16(12Q15) MUTATED     3  52
  AMP PEAK 16(12Q15) WILD-TYPE  40 252
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED      3   52
  AMP PEAK 16(12Q15) WILD-TYPE   40  252
     clus
vv    AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  NO                           3                           40
  YES                         52                          252
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, binary
                              cls
clus                             0   1
  AMP PEAK 16(12Q15) MUTATED    19  36
  AMP PEAK 16(12Q15) WILD-TYPE 112 181
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED     19   36
  AMP PEAK 16(12Q15) WILD-TYPE  112  181
        clus
vv       AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE
  FEMALE                         19                          112
  MALE                           36                          181
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12Q15) MUTATED       1                         0    52
  AMP PEAK 16(12Q15) WILD-TYPE     4                         1   274
D16V13, multiclass
                           clus
vv                          AMP PEAK 16(12Q15) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             52
                           clus
vv                          AMP PEAK 16(12Q15) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              274
[1] 3 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(12Q15) MUTATED     2  52
  AMP PEAK 16(12Q15) WILD-TYPE   5 282
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(12Q15) MUTATED      2   52
  AMP PEAK 16(12Q15) WILD-TYPE    5  282
                        clus
vv                       AMP PEAK 16(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         52
                        clus
vv                       AMP PEAK 16(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          282
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(13Q31.3) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(13Q31.3) MUTATED    36  58
  AMP PEAK 17(13Q31.3) WILD-TYPE 132 107
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                            94                            239 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                            58                            107 
$`AMP PEAK 17(13Q31.3) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A2JF 
        6.97        16.47         8.52        70.16        10.29        44.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO 
       59.57        15.25        61.38        13.32        25.78        47.87 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A6EA 
       23.11        10.22         4.18        38.93        75.65        11.31 
TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EE-A17Y TCGA-EE-A180 
       36.69         7.00         0.20        23.15        10.55         8.12 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
        5.13        60.23         9.21         7.99         9.90         8.55 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH 
        1.08        12.03         8.84         9.67        51.12        47.21 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MP 
       28.31        33.83         5.42         2.70         2.73        26.99 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
      124.31        13.81        15.95         3.22        21.60        22.22 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       33.60        12.95         5.72        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
       11.90        13.45        28.60        42.84        34.68        36.07 
TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.58        11.80         1.71        15.72         6.71         3.58 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        2.20        64.47         3.45        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 
        7.33        19.53         8.65        40.64         0.82         3.22 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK 
        2.27         0.13        16.24        15.42        10.65        14.50 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ 
       11.05        18.05       164.19         8.98        10.98        11.84 
TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-Z2-A8RT 
        7.10        21.83         1.94         8.22 

$`AMP PEAK 17(13Q31.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        3.02         6.97       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        81.24        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        86.76        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 
        6.31        92.42        56.19        64.44       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32        82.29        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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       32.28        21.44        32.61       110.24        52.01        13.68 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       17.72        29.72        22.06        15.19       142.45       108.79 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      124.47        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       21.93         5.72         9.90        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-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-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL 
       17.56        14.83        13.15         0.13        19.00        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       13.22         0.20        11.57         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C 
       12.20         4.31         4.34        15.85         1.18        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       11.15        62.79        36.85        39.62         9.50         8.09 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       49.22        36.30        36.33        34.29        17.98        60.00 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GR 
       30.08        19.43        16.01        35.54        55.69         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
       13.02        34.98        36.33         8.84        98.27         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-A2MQ 
       63.42       125.65       111.91        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       60.49        53.16        52.67         5.56       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
        3.68        30.15        12.72        22.92        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
        0.95        27.35        18.41        21.73        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       38.40        76.41        11.11       114.15        34.88         4.21 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        9.57        17.72        78.44         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       12.62        11.74         9.04         6.58        22.49         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
       18.41        85.74         5.36        13.28         4.70         3.29 
TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       11.01         7.30         3.39        20.38         8.22        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       12.16        14.70        11.84        14.50        14.50        15.81 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A828 TCGA-W3-AA1O 
        0.43         5.79         0.33         0.69        60.03         2.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.16        71.01         5.49         6.48        18.67        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       13.12         3.72         3.42         5.36         1.08        19.96 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         4.70         6.67         5.98 

  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                          0.13                           0.13 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                        164.19                         185.16 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                        11.965                         17.330 
[1] "0.1 - 164.2 (12.0)" "0.1 - 185.2 (17.3)"
[1] "hr=" "1.7"
D17V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(13Q31.3) MUTATED    36  58
  AMP PEAK 17(13Q31.3) WILD-TYPE 137 108
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                            94                            245 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                            58                            108 
$`AMP PEAK 17(13Q31.3) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2J6 TCGA-D3-A2JF 
       12.99        16.57        16.67        71.80        43.43        62.07 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO 
       59.57        58.06        86.93        60.23        26.89       137.92 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A6EA 
      125.19        11.61        58.52        89.13        95.24        25.18 
TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EE-A17Y TCGA-EE-A180 
       61.18        10.49        10.16        68.25        27.22        94.98 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
       68.15       133.81       168.26        63.35        80.61        72.07 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH 
        2.60        56.42        14.47        39.29        59.28       208.04 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MP 
       75.48        90.97        13.91        28.83       268.73       248.65 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
      124.31        13.81        23.47       172.18        64.08        53.19 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
      148.08        13.94         9.17        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
       13.02       131.51        61.05        44.05       162.08        37.25 
TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        8.88        43.82        33.21        15.72       210.08        15.16 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       34.82       216.92        48.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 
        7.79        40.27       133.55        53.16        27.09        50.14 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK 
       77.88        47.54        64.44        62.79        12.62        50.10 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ 
      294.77        18.05       212.22        63.02        42.08        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-Z2-A8RT 
        8.61        22.68        10.36        23.64 

$`AMP PEAK 17(13Q31.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       17.03        61.02       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 
       12.10       171.58        56.19        66.08       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32       166.52        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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       32.94        22.62        63.81       125.79       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       18.18        30.84        79.59        15.19       228.99       170.20 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       137.79        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         6.41        18.12        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       11.11         9.90        66.25        22.95        48.89        36.03 
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-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-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       15.68        13.87        17.85        54.02        17.29        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-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C 
       26.89         4.96       151.27        91.56        13.55        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       13.97        63.78        64.64        56.84        18.61        37.35 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       55.92       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        36.82        86.14        67.43       314.56       161.03 
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       126.81        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       158.63       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 
      134.40       162.48        71.21        53.26       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
        3.68        54.51       138.81       127.20        36.95        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       109.58        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       50.76        77.75        26.37       268.93       152.35         6.44 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89       148.18        79.99        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       31.27        32.05       247.04        80.32        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
       92.98       174.21         7.00        38.27        29.46        94.39 
TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
      228.59        27.72        48.85       357.37        53.52        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
       11.41       148.80        26.56        49.48        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       32.48        39.58        46.36        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A828 TCGA-W3-AA1O 
      357.04         6.67         0.33         0.69       121.08         4.01 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        38.56        54.38        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       59.41        52.34         3.75        43.73         2.20        30.18 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        14.43        93.07        11.74 

  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                          2.60                           0.16 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                        294.77                         369.93 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                         51.65                          49.48 
[1] "2.6 - 294.8 (51.6)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.4"
D17V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 17(13Q31.3) MUTATED                   23             2
  AMP PEAK 17(13Q31.3) WILD-TYPE                 38             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 17(13Q31.3) MUTATED                                          21
  AMP PEAK 17(13Q31.3) WILD-TYPE                                        51
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 17(13Q31.3) MUTATED                    53
  AMP PEAK 17(13Q31.3) WILD-TYPE                 156
D17V4, multiclass
                                           clus
vv                                          AMP PEAK 17(13Q31.3) MUTATED
  DISTANT METASTASIS                                                  23
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           21
  REGIONAL LYMPH NODE                                                 53
                                           clus
vv                                          AMP PEAK 17(13Q31.3) WILD-TYPE
  DISTANT METASTASIS                                                    38
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             51
  REGIONAL LYMPH NODE                                                  156
[1] 4 2
[1] 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(13Q31.3) MUTATED             3       1      11        3       12
  AMP PEAK 17(13Q31.3) WILD-TYPE           9       6      17       14       15
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 17(13Q31.3) MUTATED          5         1         7         6
  AMP PEAK 17(13Q31.3) WILD-TYPE       17        13        12         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 17(13Q31.3) MUTATED           6          4         11         16
  AMP PEAK 17(13Q31.3) WILD-TYPE        29         11         21         42
                                vv
clus                             STAGE IV
  AMP PEAK 17(13Q31.3) MUTATED          4
  AMP PEAK 17(13Q31.3) WILD-TYPE       15
D17V5, multiclass
             clus
vv            AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE
  I OR II NOS                            3                              9
  STAGE 0                                1                              6
  STAGE I                               11                             17
  STAGE IA                               3                             14
  STAGE IB                              12                             15
  STAGE II                               5                             17
  STAGE IIA                              1                             13
  STAGE IIB                              7                             12
  STAGE IIC                              6                              6
  STAGE III                              6                             29
  STAGE IIIA                             4                             11
  STAGE IIIB                            11                             21
  STAGE IIIC                            16                             42
  STAGE IV                               4                             15
[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(13Q31.3) MUTATED      16 26 14 23
  AMP PEAK 17(13Q31.3) WILD-TYPE    47 45 60 44
D17V6, multiclass
       clus
vv      AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE
  T0+T1                           16                             47
  T2                              26                             45
  T3                              14                             60
  T4                              23                             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 17(13Q31.3) MUTATED    52  17   7  13
  AMP PEAK 17(13Q31.3) WILD-TYPE 116  44  31  34
D17V7, multiclass
    clus
vv   AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE
  N0                           52                            116
  N1                           17                             44
  N2                            7                             31
  N3                           13                             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
  AMP PEAK 17(13Q31.3) MUTATED    87   1   2   0   1
  AMP PEAK 17(13Q31.3) WILD-TYPE 219   3   1   4   8
D17V8, multiclass
     clus
vv    AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE
  M0                            87                            219
  M1                             1                              3
  M1A                            2                              1
  M1B                            0                              4
  M1C                            1                              8
[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(13Q31.3) MUTATED   32 28
  AMP PEAK 17(13Q31.3) WILD-TYPE 97 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q31.3) MUTATED     32   28
  AMP PEAK 17(13Q31.3) WILD-TYPE   97   59
     clus
vv    AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE
  NO                            32                             97
  YES                           28                             59
[1] 2 2
[1] FALSE
D17V10, binary
                                cls
clus                               0   1
  AMP PEAK 17(13Q31.3) MUTATED    14  86
  AMP PEAK 17(13Q31.3) WILD-TYPE  29 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q31.3) MUTATED     14   86
  AMP PEAK 17(13Q31.3) WILD-TYPE   29  218
     clus
vv    AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE
  NO                            14                             29
  YES                           86                            218
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, binary
                                cls
clus                               0   1
  AMP PEAK 17(13Q31.3) MUTATED    35  65
  AMP PEAK 17(13Q31.3) WILD-TYPE  96 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q31.3) MUTATED     35   65
  AMP PEAK 17(13Q31.3) WILD-TYPE   96  152
        clus
vv       AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE
  FEMALE                           35                             96
  MALE                             65                            152
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(13Q31.3) MUTATED       2                         0    94
  AMP PEAK 17(13Q31.3) WILD-TYPE     3                         1   232
D17V13, multiclass
                           clus
vv                          AMP PEAK 17(13Q31.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               94
                           clus
vv                          AMP PEAK 17(13Q31.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                232
[1] 3 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(13Q31.3) MUTATED     1  95
  AMP PEAK 17(13Q31.3) WILD-TYPE   6 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(13Q31.3) MUTATED      1   95
  AMP PEAK 17(13Q31.3) WILD-TYPE    6  239
                        clus
vv                       AMP PEAK 17(13Q31.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           95
                        clus
vv                       AMP PEAK 17(13Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            239
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(15Q26.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(15Q26.2) MUTATED    52  56
  AMP PEAK 18(15Q26.2) WILD-TYPE 116 109
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                           108                            225 
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                            56                            109 
$`AMP PEAK 18(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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MU 
       44.19        92.42        56.19        82.29        13.32        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI 
       29.23        93.21        32.28        29.72        10.22         4.18 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       38.93        75.65        11.44        21.93         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        60.23        15.85         9.21 
TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2GH 
       11.15        30.44        32.15         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        55.69         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        60.49        53.16       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        21.73        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-A19T TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
        6.58         6.58        22.49         5.62        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        6.71         5.36         2.20         4.70        14.24         7.33 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZY 
       20.38         8.22        12.92        52.08         8.65         0.82 
TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
        3.22         2.27         0.99         7.23        11.61        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       84.72        16.24        12.16        14.50        14.50        14.50 
TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-Z2-AA3V 
        8.98         2.99         7.10         3.72        21.83         5.98 

$`AMP PEAK 18(15Q26.2) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       85.32         8.38        68.22         7.50        36.16         6.31 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51F 
       61.38        24.00         6.31         9.34       103.59        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       31.30        54.31        21.44        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC 
       52.01        47.87        13.68        17.72        23.11        22.06 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
       15.19       142.45       108.79       124.47        87.62         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
       24.07         4.01         5.72        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-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
        0.13        23.15        19.00        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
       11.57         6.31         1.12         1.35         5.13         4.31 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        4.34         1.18         7.99         9.90        37.97        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 
        8.09         8.84         9.99         2.43        11.31        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       19.43        16.01        35.54         1.15        13.02        34.98 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        8.84         6.18        47.51        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT 
        7.96        14.56       125.65       111.91        56.02        52.67 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 
        5.56        51.62         3.68        12.72        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 
       16.14        22.22         0.95        27.35        18.41        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E 
       12.95        38.40         5.72        76.41        25.18        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       11.11       114.15        34.88         4.21        13.45        42.84 
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-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
       13.08        12.62        11.74         9.04         1.71        18.41 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        3.58        13.28         3.29        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF 
       23.80        15.52         7.30         3.39        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.17        30.87        12.89        47.38         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64         8.68        27.39         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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
        0.13         0.16        17.33         9.90         0.85        44.28 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-HR-A2OH 
       10.13        15.42        14.70        11.84        10.65        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
        0.43        11.05         5.79        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      164.19        60.03        10.98       185.16        71.01        11.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
        5.49         6.48        18.67        21.07        13.12         3.42 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36         1.08        19.96         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        4.70         8.22         6.67 

  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                          0.82                           0.13 
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                        124.31                         185.16 
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                         18.97                          13.68 
[1] "0.8 - 124.3 (19.0)" "0.1 - 185.2 (13.7)"
[1] "hr=" "1"  
D18V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(15Q26.2) MUTATED    54  56
  AMP PEAK 18(15Q26.2) WILD-TYPE 119 110
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                           110                            229 
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                            56                            110 
$`AMP PEAK 18(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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MU 
       62.07       171.58        56.19       166.52        60.23        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI 
       45.30       174.84        32.94        30.84        11.61        58.52 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
       89.13        95.24        29.06       151.53        54.67        22.29 
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       133.81 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       91.56       168.26        13.97       369.93       195.02        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       126.81 
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       134.40       162.48       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 
      109.58       148.08        31.40        48.89        12.59        61.05 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
      162.08        37.25         8.88        80.32        46.98         6.77 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
      174.21        15.72       210.08         7.00        34.82        29.46 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       20.91         7.79       357.37        53.52        47.38        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GF-A4EO 
      133.55        27.09        50.14        77.88        22.92         7.23 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK 
       11.74       117.93        84.72        64.44        32.48        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8K6 TCGA-WE-A8ZQ 
       21.37        59.41        63.02         4.01         8.61        52.34 
TCGA-WE-A8ZX TCGA-Z2-AA3V 
       22.68        11.74 

$`AMP PEAK 18(15Q26.2) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      103.10        65.49       168.00       113.52        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51F 
       86.93        24.53        13.87         9.34       103.59        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       56.35       145.12        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC 
      135.75       137.92       178.32        18.18       125.19        79.59 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
       15.19       228.99       170.20       161.00       137.79       129.63 
TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      117.17         3.65         6.41        18.12        11.34        11.11 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       66.25        22.95       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       28.60        15.68        10.16        17.85        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       17.29        52.01         6.35        12.20        29.82         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I 
       33.73        14.70        68.15         4.96       151.27        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       55.92        25.87        46.82        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28        67.43       314.56       161.03        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 
       79.66        14.30        55.59        44.88        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
      158.63       203.05       167.90        71.21        53.26        51.62 
TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.68       138.81       127.20        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      201.80        27.35        51.35        35.44        13.94        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-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
      152.35         6.44       131.51        44.05        50.89       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-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA 
       32.05       247.04        33.21        92.98        15.16        38.27 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       94.39       216.92        48.59       228.59       202.65        28.08 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       23.93       101.26        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       12.43        26.73        49.45         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
       19.30         9.90         2.04       139.89        10.13        62.79 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       39.58        46.36        12.62        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        6.67        18.05         0.33         0.69       212.22       121.08 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        38.56        54.38 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       90.28        56.98        59.41         3.75        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       30.18        10.36        15.16        36.03        14.43        23.64 
TCGA-Z2-AA3S 
       93.07 

  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                          4.01                           0.16 
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                        369.93                         357.04 
  AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE 
                         51.24                          49.48 
[1] "4.0 - 369.9 (51.2)" "0.2 - 357.0 (49.5)"
[1] "hr=" "1"  
D18V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 18(15Q26.2) MUTATED                   17             3
  AMP PEAK 18(15Q26.2) WILD-TYPE                 44             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 18(15Q26.2) MUTATED                                          19
  AMP PEAK 18(15Q26.2) WILD-TYPE                                        53
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 18(15Q26.2) MUTATED                    77
  AMP PEAK 18(15Q26.2) WILD-TYPE                 132
D18V4, multiclass
                                           clus
vv                                          AMP PEAK 18(15Q26.2) MUTATED
  DISTANT METASTASIS                                                  17
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           19
  REGIONAL LYMPH NODE                                                 77
                                           clus
vv                                          AMP PEAK 18(15Q26.2) WILD-TYPE
  DISTANT METASTASIS                                                    44
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             53
  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
  AMP PEAK 18(15Q26.2) MUTATED            10       2      11        7        7
  AMP PEAK 18(15Q26.2) WILD-TYPE           2       5      17       10       20
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 18(15Q26.2) MUTATED          9         3         4         4
  AMP PEAK 18(15Q26.2) WILD-TYPE       13        11        15         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 18(15Q26.2) MUTATED          12          7         15         14
  AMP PEAK 18(15Q26.2) WILD-TYPE        23          8         17         44
                                vv
clus                             STAGE IV
  AMP PEAK 18(15Q26.2) MUTATED          3
  AMP PEAK 18(15Q26.2) WILD-TYPE       16
D18V5, multiclass
             clus
vv            AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE
  I OR II NOS                           10                              2
  STAGE 0                                2                              5
  STAGE I                               11                             17
  STAGE IA                               7                             10
  STAGE IB                               7                             20
  STAGE II                               9                             13
  STAGE IIA                              3                             11
  STAGE IIB                              4                             15
  STAGE IIC                              4                              8
  STAGE III                             12                             23
  STAGE IIIA                             7                              8
  STAGE IIIB                            15                             17
  STAGE IIIC                            14                             44
  STAGE IV                               3                             16
[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(15Q26.2) MUTATED      24 24 24 18
  AMP PEAK 18(15Q26.2) WILD-TYPE    39 47 50 49
D18V6, multiclass
       clus
vv      AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE
  T0+T1                           24                             39
  T2                              24                             47
  T3                              24                             50
  T4                              18                             49
[1] 4 2
[1] 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(15Q26.2) MUTATED    58  20  14  13
  AMP PEAK 18(15Q26.2) WILD-TYPE 110  41  24  34
D18V7, multiclass
    clus
vv   AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE
  N0                           58                            110
  N1                           20                             41
  N2                           14                             24
  N3                           13                             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
  AMP PEAK 18(15Q26.2) MUTATED   105   1   1   1   1
  AMP PEAK 18(15Q26.2) WILD-TYPE 201   3   2   3   8
D18V8, multiclass
     clus
vv    AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE
  M0                           105                            201
  M1                             1                              3
  M1A                            1                              2
  M1B                            1                              3
  M1C                            1                              8
[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(15Q26.2) MUTATED   42 22
  AMP PEAK 18(15Q26.2) WILD-TYPE 87 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(15Q26.2) MUTATED     42   22
  AMP PEAK 18(15Q26.2) WILD-TYPE   87   65
     clus
vv    AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE
  NO                            42                             87
  YES                           22                             65
[1] 2 2
[1] FALSE
D18V10, binary
                                cls
clus                               0   1
  AMP PEAK 18(15Q26.2) MUTATED    18  97
  AMP PEAK 18(15Q26.2) WILD-TYPE  25 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(15Q26.2) MUTATED     18   97
  AMP PEAK 18(15Q26.2) WILD-TYPE   25  207
     clus
vv    AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE
  NO                            18                             25
  YES                           97                            207
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, binary
                                cls
clus                               0   1
  AMP PEAK 18(15Q26.2) MUTATED    46  70
  AMP PEAK 18(15Q26.2) WILD-TYPE  85 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(15Q26.2) MUTATED     46   70
  AMP PEAK 18(15Q26.2) WILD-TYPE   85  147
        clus
vv       AMP PEAK 18(15Q26.2) MUTATED AMP PEAK 18(15Q26.2) WILD-TYPE
  FEMALE                           46                             85
  MALE                             70                            147
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(15Q26.2) MUTATED       2                         0   111
  AMP PEAK 18(15Q26.2) WILD-TYPE     3                         1   215
D18V13, multiclass
                           clus
vv                          AMP PEAK 18(15Q26.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              111
                           clus
vv                          AMP PEAK 18(15Q26.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                215
[1] 3 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(15Q26.2) MUTATED     2 112
  AMP PEAK 18(15Q26.2) WILD-TYPE   5 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(15Q26.2) MUTATED      2  112
  AMP PEAK 18(15Q26.2) WILD-TYPE    5  222
                        clus
vv                       AMP PEAK 18(15Q26.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       AMP PEAK 18(15Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            222
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(17Q25.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(17Q25.3) MUTATED    58  57
  AMP PEAK 19(17Q25.3) WILD-TYPE 110 108
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                           115                            218 
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                            57                            108 
$`AMP PEAK 19(17Q25.3) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q9 
        3.02         6.97        16.47         8.52       111.09        22.55 
TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JL 
       45.83        68.22        86.76        11.41        44.19        92.42 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
      114.67        15.25        61.38        24.00         9.34        29.23 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GM 
       21.44        25.78        17.72        29.72        22.06        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HY 
      124.47        87.62        11.44         9.90        48.79        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 
       39.19        36.69         4.93         6.64         7.00        17.56 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        0.20        13.35        10.55         1.12         1.35         5.13 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
        4.31        15.85         9.21        11.15        36.85         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GB 
        9.50        12.03         8.84         2.43        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR 
       34.29        47.21        30.08        28.31         5.42         1.15 
TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MN TCGA-EE-A2MP 
        2.70         9.53         7.96        14.56        25.08        26.99 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 
       60.49        53.16        52.67        51.62        30.15        21.60 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19N 
       22.22        21.73        33.60         3.78        11.11        42.84 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A3ET 
        9.57         6.58        17.72        11.80         1.51         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YW 
       22.49         1.71        18.41         5.36         2.20        64.47 
TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT 
        3.45         8.22        12.89        47.38         8.65        40.64 
TCGA-FS-A1ZU TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
        8.68         2.27         0.20        84.72        15.42        14.70 
TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O 
       14.50         5.79         0.69       164.19         8.98         2.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-AA9Y TCGA-WE-AAA0 
      185.16        71.01        11.84         5.49         1.08        19.96 
TCGA-WE-AAA3 
        1.94 

$`AMP PEAK 19(17Q25.3) WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
        6.97        32.42        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-A2JG 
       10.29        85.32         8.38        21.14        88.50         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
       36.16         6.31        56.19        64.44        59.57        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU 
       46.32        82.29        13.32         6.31       103.59        26.37 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       93.21        54.74        31.30        54.31        32.28        32.61 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD 
      110.24        52.01        47.87        13.68        23.11        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR 
       15.19         4.18       142.45       108.79        38.93         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
       24.07         4.01        21.93         5.72        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       14.60        35.80        10.03        13.68         9.99        44.52 
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-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       23.15        19.00        13.22         0.20        11.57         6.31 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A 
        8.12        12.20        60.23         4.34         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29Q 
        9.90        37.97        62.79         8.55        39.62         8.09 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99        30.44        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       36.30         9.67        17.98        60.00        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       35.54        33.83        55.69        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
        8.84        98.27         6.18        47.51        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ 
       44.25        63.42       125.65       111.91        56.02        21.60 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
        5.56       124.31       122.73         3.68        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       12.72         3.22        22.92        21.60        16.14         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35        18.41        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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
        5.62        85.74        15.72         6.71         3.58        13.28 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.70         3.29        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-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.17        30.87        12.92        52.08         8.81        49.15 
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-FW-A3R5 
       28.73        14.20        10.78         5.98         6.41         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       11.61        44.28        31.33        10.13        16.24        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB 
       11.84        10.65        14.50        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8K5 
       11.05        18.05         0.33        60.03        10.98         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        7.10        18.67        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       21.83         5.36        12.07         6.18         4.70         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                          0.20                           0.13 
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                        185.16                         142.45 
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                         15.25                          14.55 
[1] "0.2 - 185.2 (15.2)" "0.1 - 142.4 (14.6)"
[1] "hr=" "1"  
D19V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(17Q25.3) MUTATED    60  57
  AMP PEAK 19(17Q25.3) WILD-TYPE 113 109
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                           117                            222 
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                            57                            109 
$`AMP PEAK 19(17Q25.3) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q9 
       17.03        61.02        16.57        16.67       112.04        31.59 
TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JL 
       90.90       168.00        86.76        11.87        62.07       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
      130.72        58.06        86.93        24.53         9.34        45.30 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GM 
       22.62        26.89        18.18        30.84        79.59        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 
      161.00       137.79        29.06       151.53         3.65         9.90 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       48.89       117.21       194.83        61.18        65.92        68.09 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 
       10.49       215.44        10.16        17.29        27.22        33.73 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29D 
       14.70        68.15         4.96        91.56       168.26        13.97 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29V 
       64.64         2.60        18.61        56.42        14.47        25.87 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
       86.14        59.28        67.43       208.04        48.72        75.48 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MI 
       13.91        14.30        28.83        47.28        16.96       204.66 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
       47.54       248.65       134.40       162.48        71.21        51.62 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19C 
       54.51        36.95        53.19       109.58       148.08        48.89 
TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC 
       26.37        44.05        50.89         8.88       148.18        43.82 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U9 
       20.15        80.32        46.98        33.21        92.98         7.00 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM 
       34.82       216.92        48.59        53.52        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A265 
      133.55        53.16        26.56        77.88         0.20        84.72 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A824 
       62.79        39.58        59.41         6.67         0.69       212.22 
TCGA-W3-A825 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       63.02         4.01       219.16       105.04        24.03        38.56 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        2.20        30.18        10.36 

$`AMP PEAK 19(17Q25.3) WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       12.99       112.57        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-A2JG 
       43.43       103.10        65.49        23.77       115.53       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
       42.08        12.10        56.19        66.08        59.57        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU 
       46.32       166.52        60.23        13.87       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      174.84        55.73        56.35       145.12        32.94        63.81 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GD 
      125.79       135.75       137.92       178.32       125.19        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GR 
       15.19        58.52       228.99       170.20        89.13       129.63 
TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      117.17        54.67         6.41        18.12        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 
       11.11        25.18        66.25        22.95        36.03        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 
      176.55        35.93       107.34        53.92        23.44        28.60 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       15.68        13.87        17.85        68.25        54.02        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 
        6.35        12.20        29.82         8.65        94.98        26.89 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      133.81       151.27        13.55        63.35        80.61        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       63.78        72.07        56.84        37.35        55.92       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      314.56       161.03        89.33        54.74        79.66        90.97 
TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
      126.81        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ 
       19.76        61.51       103.27       268.73       103.20        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA 
      158.63       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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        64.08        34.32       201.80        27.35        51.35 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        12.59        13.02       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND 
      131.51        61.05       162.08        37.25        79.99        23.34 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A44A 
       16.37        31.27        32.05       247.04         6.77       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
       15.72       210.08        15.16        38.27        29.46        94.39 
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-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-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
       47.38        74.73        11.41       148.80        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       12.43        26.73        49.45        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O 
       50.10        21.37        65.88       357.04       294.77        18.05 
TCGA-RP-A693 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
        0.33       121.08        42.08        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       56.98        59.41        52.34         3.75        22.68        43.73 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        14.43        23.64        93.07        11.74 

  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                          0.20                           0.16 
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                        248.65                         369.93 
  AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE 
                         48.89                          50.45 
[1] "0.2 - 248.7 (48.9)" "0.2 - 369.9 (50.5)"
[1] "hr=" "1.1"
D19V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 19(17Q25.3) MUTATED                   23             2
  AMP PEAK 19(17Q25.3) WILD-TYPE                 38             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 19(17Q25.3) MUTATED                                          17
  AMP PEAK 19(17Q25.3) WILD-TYPE                                        55
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 19(17Q25.3) MUTATED                    76
  AMP PEAK 19(17Q25.3) WILD-TYPE                 133
D19V4, multiclass
                                           clus
vv                                          AMP PEAK 19(17Q25.3) MUTATED
  DISTANT METASTASIS                                                  23
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           17
  REGIONAL LYMPH NODE                                                 76
                                           clus
vv                                          AMP PEAK 19(17Q25.3) WILD-TYPE
  DISTANT METASTASIS                                                    38
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             55
  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
  AMP PEAK 19(17Q25.3) MUTATED             5       2      11        8        9
  AMP PEAK 19(17Q25.3) WILD-TYPE           7       5      17        9       18
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 19(17Q25.3) MUTATED          9         2         6         6
  AMP PEAK 19(17Q25.3) WILD-TYPE       13        12        13         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 19(17Q25.3) MUTATED          11          2         13         21
  AMP PEAK 19(17Q25.3) WILD-TYPE        24         13         19         37
                                vv
clus                             STAGE IV
  AMP PEAK 19(17Q25.3) MUTATED          6
  AMP PEAK 19(17Q25.3) WILD-TYPE       13
D19V5, multiclass
             clus
vv            AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE
  I OR II NOS                            5                              7
  STAGE 0                                2                              5
  STAGE I                               11                             17
  STAGE IA                               8                              9
  STAGE IB                               9                             18
  STAGE II                               9                             13
  STAGE IIA                              2                             12
  STAGE IIB                              6                             13
  STAGE IIC                              6                              6
  STAGE III                             11                             24
  STAGE IIIA                             2                             13
  STAGE IIIB                            13                             19
  STAGE IIIC                            21                             37
  STAGE IV                               6                             13
[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(17Q25.3) MUTATED      22 30 21 26
  AMP PEAK 19(17Q25.3) WILD-TYPE    41 41 53 41
D19V6, multiclass
       clus
vv      AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE
  T0+T1                           22                             41
  T2                              30                             41
  T3                              21                             53
  T4                              26                             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
  AMP PEAK 19(17Q25.3) MUTATED    60  19  15  16
  AMP PEAK 19(17Q25.3) WILD-TYPE 108  42  23  31
D19V7, multiclass
    clus
vv   AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE
  N0                           60                            108
  N1                           19                             42
  N2                           15                             23
  N3                           16                             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 19(17Q25.3) MUTATED   107   1   2   1   3
  AMP PEAK 19(17Q25.3) WILD-TYPE 199   3   1   3   6
D19V8, multiclass
     clus
vv    AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE
  M0                           107                            199
  M1                             1                              3
  M1A                            2                              1
  M1B                            1                              3
  M1C                            3                              6
[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(17Q25.3) MUTATED   40 33
  AMP PEAK 19(17Q25.3) WILD-TYPE 89 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q25.3) MUTATED     40   33
  AMP PEAK 19(17Q25.3) WILD-TYPE   89   54
     clus
vv    AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE
  NO                            40                             89
  YES                           33                             54
[1] 2 2
[1] FALSE
D19V10, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q25.3) MUTATED    15 103
  AMP PEAK 19(17Q25.3) WILD-TYPE  28 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q25.3) MUTATED     15  103
  AMP PEAK 19(17Q25.3) WILD-TYPE   28  201
     clus
vv    AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE
  NO                            15                             28
  YES                          103                            201
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q25.3) MUTATED    37  81
  AMP PEAK 19(17Q25.3) WILD-TYPE  94 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q25.3) MUTATED     37   81
  AMP PEAK 19(17Q25.3) WILD-TYPE   94  136
        clus
vv       AMP PEAK 19(17Q25.3) MUTATED AMP PEAK 19(17Q25.3) WILD-TYPE
  FEMALE                           37                             94
  MALE                             81                            136
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(17Q25.3) MUTATED       2                         1   111
  AMP PEAK 19(17Q25.3) WILD-TYPE     3                         0   215
D19V13, multiclass
                           clus
vv                          AMP PEAK 19(17Q25.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              111
                           clus
vv                          AMP PEAK 19(17Q25.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                215
[1] 3 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(17Q25.3) MUTATED     1 115
  AMP PEAK 19(17Q25.3) WILD-TYPE   6 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q25.3) MUTATED      1  115
  AMP PEAK 19(17Q25.3) WILD-TYPE    6  219
                        clus
vv                       AMP PEAK 19(17Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          115
                        clus
vv                       AMP PEAK 19(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            219
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(19P13.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(19P13.2) MUTATED    34  32
  AMP PEAK 20(19P13.2) WILD-TYPE 134 133
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            66                            267 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            32                            133 
$`AMP PEAK 20(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        86.76        44.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A5GU TCGA-D3-A8GI 
       64.44        59.57        26.37        32.61        23.11         4.18 
TCGA-D3-A8GM TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-DA-A3F5 
       75.65         9.90        13.22        10.03         6.64        17.56 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       10.55         8.12        62.79         1.08        12.03         8.84 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MM 
       47.21        55.69        98.27         2.70        44.25        56.02 
TCGA-EE-A2MR TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19J 
       60.49        22.92        33.60         5.72        11.90         4.21 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 
        6.58         1.87         6.58         1.71        18.41         6.71 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        3.45        11.01        14.24         7.33        20.38         8.22 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 
       12.92        47.38        49.15         3.22        28.73         0.20 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8ZQ 
       11.61        10.13        16.24         8.98        71.01         3.72 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3S 
       21.83         5.36         1.08         1.94         6.18         6.67 

$`AMP PEAK 20(19P13.2) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        28.08        22.55        45.83        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
        8.38        21.14        68.22        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
        6.31        92.42        56.19       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       54.31        32.28        21.44        25.78       110.24        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       47.87        13.68        17.72        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       15.19       142.45       108.79        38.93       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       11.44         5.56        24.07         4.01        21.93         5.72 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       11.31        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-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       22.36        19.36         7.00        14.83        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
        0.13        23.15        19.00        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57         6.31         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       39.62         9.50         8.09         9.99        30.44         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       36.33        51.12        34.29        17.98        60.00        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-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
        1.15        13.02        34.98        36.33         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46         2.73         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       63.42       125.65       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 
       53.16        52.67         5.56       124.31       122.73        51.62 
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-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        31.40        18.61        12.95        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-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       36.07        17.72        78.44        11.80         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A 
       12.62        11.74         9.04        22.49         5.62        85.74 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72         3.58         5.36        13.28         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        3.29        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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        31.33        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       15.42        12.16        14.70        11.84        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33         0.69       164.19        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       10.98       185.16        11.84         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       18.67        21.07        13.12         3.42        19.96        12.07 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
        4.70         8.22         5.98 

  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                          0.20                           0.13 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                         98.27                         185.16 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                        12.475                         15.250 
[1] "0.2 - 98.3 (12.5)"  "0.1 - 185.2 (15.2)"
[1] "hr=" "1"  
D20V2, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(19P13.2) MUTATED    34  32
  AMP PEAK 20(19P13.2) WILD-TYPE 139 134
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            66                            273 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            32                            134 
$`AMP PEAK 20(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        86.76        62.07 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A5GU TCGA-D3-A8GI 
       66.08        59.57        39.75        63.81       125.19        58.52 
TCGA-D3-A8GM TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-DA-A3F5 
       95.24         9.90        66.25        20.38        68.09       215.44 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       27.22        94.98        63.78         2.60        56.42        14.47 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MM 
      208.04       126.81       129.27        28.83       103.20       167.90 
TCGA-EE-A2MR TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19J 
      134.40       127.20       148.08         9.17        13.02         6.44 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 
        8.88        23.34        80.32        33.21        92.98       210.08 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       48.59       228.59        20.91         7.79       357.37        53.52 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 
       47.38       101.26       148.80        50.14        28.73         0.20 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8ZQ 
       11.74        10.13        64.44        63.02       105.04        52.34 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3S 
       22.68        43.73         2.20        10.36        36.03        93.07 

$`AMP PEAK 20(19P13.2) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        31.59        90.90        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       65.49        23.77       168.00        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       12.10       171.58        56.19       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        22.62        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      137.92       178.32        18.18        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       15.19       228.99       170.20        89.13       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
        6.41        18.12        11.34        22.29        11.11        25.18 
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-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       28.60        10.49        15.68        13.87        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82         8.65        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        13.97        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.84        18.61        37.35        55.92       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       86.14        59.28        67.43       314.56       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       89.33        54.74        79.66        75.48        90.97        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
       14.30        55.59        44.88        94.82        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       158.63       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 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       109.58        31.40        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       77.75        98.40        48.89        12.59        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A 
       31.27        32.05       247.04        46.98         6.77       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72        15.16         7.00        38.27        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       94.39       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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       62.79        32.48        39.58        46.36        12.62        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       21.37        59.41        65.88       357.04       294.77         6.67 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33         0.69       212.22       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16        24.03        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       90.28        56.98        59.41         3.75        30.18        15.16 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
       14.43        23.64        11.74 

  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                          0.20                           0.16 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                        357.37                         369.93 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                        62.545                         48.720 
[1] "0.2 - 357.4 (62.5)" "0.2 - 369.9 (48.7)"
[1] "hr=" "1.1"
D20V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 20(19P13.2) MUTATED                   10             3
  AMP PEAK 20(19P13.2) WILD-TYPE                 51             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 20(19P13.2) MUTATED                                          16
  AMP PEAK 20(19P13.2) WILD-TYPE                                        56
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 20(19P13.2) MUTATED                    38
  AMP PEAK 20(19P13.2) WILD-TYPE                 171
D20V4, multiclass
                                           clus
vv                                          AMP PEAK 20(19P13.2) MUTATED
  DISTANT METASTASIS                                                  10
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           16
  REGIONAL LYMPH NODE                                                 38
                                           clus
vv                                          AMP PEAK 20(19P13.2) WILD-TYPE
  DISTANT METASTASIS                                                    51
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             56
  REGIONAL LYMPH NODE                                                  171
[1] 4 2
[1] 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(19P13.2) MUTATED             2       0      11        3        4
  AMP PEAK 20(19P13.2) WILD-TYPE          10       7      17       14       23
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 20(19P13.2) MUTATED          4         5         1         2
  AMP PEAK 20(19P13.2) WILD-TYPE       18         9        18        10
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 20(19P13.2) MUTATED           5          6          5         10
  AMP PEAK 20(19P13.2) WILD-TYPE        30          9         27         48
                                vv
clus                             STAGE IV
  AMP PEAK 20(19P13.2) MUTATED          6
  AMP PEAK 20(19P13.2) WILD-TYPE       13
D20V5, multiclass
             clus
vv            AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  I OR II NOS                            2                             10
  STAGE 0                                0                              7
  STAGE I                               11                             17
  STAGE IA                               3                             14
  STAGE IB                               4                             23
  STAGE II                               4                             18
  STAGE IIA                              5                              9
  STAGE IIB                              1                             18
  STAGE IIC                              2                             10
  STAGE III                              5                             30
  STAGE IIIA                             6                              9
  STAGE IIIB                             5                             27
  STAGE IIIC                            10                             48
  STAGE IV                               6                             13
[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(19P13.2) MUTATED      11 16 18 12
  AMP PEAK 20(19P13.2) WILD-TYPE    52 55 56 55
D20V6, multiclass
       clus
vv      AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  T0+T1                           11                             52
  T2                              16                             55
  T3                              18                             56
  T4                              12                             55
[1] 4 2
[1] 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(19P13.2) MUTATED    35  11   6  10
  AMP PEAK 20(19P13.2) WILD-TYPE 133  50  32  37
D20V7, multiclass
    clus
vv   AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  N0                           35                            133
  N1                           11                             50
  N2                            6                             32
  N3                           10                             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                              M0  M1 M1A M1B M1C
  AMP PEAK 20(19P13.2) MUTATED    57   3   3   0   0
  AMP PEAK 20(19P13.2) WILD-TYPE 249   1   0   4   9
D20V8, multiclass
     clus
vv    AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  M0                            57                            249
  M1                             3                              1
  M1A                            3                              0
  M1B                            0                              4
  M1C                            0                              9
[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(19P13.2) MUTATED   30 14
  AMP PEAK 20(19P13.2) WILD-TYPE 99 73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     30   14
  AMP PEAK 20(19P13.2) WILD-TYPE   99   73
     clus
vv    AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  NO                            30                             99
  YES                           14                             73
[1] 2 2
[1] FALSE
D20V10, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED     9  58
  AMP PEAK 20(19P13.2) WILD-TYPE  34 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED      9   58
  AMP PEAK 20(19P13.2) WILD-TYPE   34  246
     clus
vv    AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  NO                             9                             34
  YES                           58                            246
[1] 2 2
[1] FALSE
D20V11, continuous
D20V12, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED    24  43
  AMP PEAK 20(19P13.2) WILD-TYPE 107 174
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     24   43
  AMP PEAK 20(19P13.2) WILD-TYPE  107  174
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  FEMALE                           24                            107
  MALE                             43                            174
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(19P13.2) MUTATED       1                         0    59
  AMP PEAK 20(19P13.2) WILD-TYPE     4                         1   267
D20V13, multiclass
                           clus
vv                          AMP PEAK 20(19P13.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               59
                           clus
vv                          AMP PEAK 20(19P13.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                267
[1] 3 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(19P13.2) MUTATED     1  64
  AMP PEAK 20(19P13.2) WILD-TYPE   6 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED      1   64
  AMP PEAK 20(19P13.2) WILD-TYPE    6  270
                        clus
vv                       AMP PEAK 20(19P13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       AMP PEAK 20(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(20Q13.33) MUTATION ANALYSIS
D21V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 21(20Q13.33) MUTATED   89 85
  AMP PEAK 21(20Q13.33) WILD-TYPE 79 80
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                            174                             159 
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                             85                              80 
$`AMP PEAK 21(20Q13.33) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 
        3.02         6.97        16.47        32.42        22.55        21.14 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        86.76        11.41        44.19         7.50        36.16 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       92.42        56.19        59.57        15.25        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K 
       13.32       103.59        26.37        29.23        54.31        32.28 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       32.61        52.01        47.87        13.68        23.11        22.06 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       10.22         4.18       108.79        38.93        75.65        87.62 
TCGA-D3-A8GQ TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW 
       11.44        21.93         9.90        11.31        13.22        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A5SH 
       10.03        13.68        36.69         4.93        17.56        19.00 
TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 
       13.35         0.20        10.55         8.12        12.20         5.13 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
       60.23         9.21         7.99        11.15        62.79         1.08 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
       12.03         8.84        30.44        32.15         8.09        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        9.67        36.33        51.12        60.00        47.21        30.08 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 
       28.31        33.83        55.69         5.42        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MH 
       98.27         2.70         6.18        47.51        44.25         7.96 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       26.99        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
       51.62         3.68        30.15        15.95         3.22        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       21.60        22.22         0.95        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A2NC 
       13.45        28.60        34.68         6.58        17.72        11.80 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        1.87        12.62         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       15.72         6.71         4.70         3.45        23.80        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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.92        12.89        47.38         8.65        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD 
        8.68         0.82         3.22        28.73        14.20         2.27 
TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.20         7.23        11.61        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       15.42        12.16        14.70        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        15.81         0.43        11.05         5.79        18.05 
TCGA-W3-A825 TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM 
        8.98       185.16        71.01        11.84         7.10        18.67 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
        3.72        21.83         5.36         1.94         6.18         4.70 

$`AMP PEAK 21(20Q13.33) WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        6.97         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-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF 
        6.31        64.44       114.67        46.98        46.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N 
        6.31         9.34        93.21        54.74        31.30        21.44 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
       25.78       110.24        17.72        29.72        15.19       142.45 
TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG 
      124.47         5.56        24.07         4.01         5.72        14.60 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       48.79        51.12        39.19         9.99        44.52        25.15 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z 
        0.20         0.13        23.15        13.22        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
        1.12         1.35         4.31         4.34        15.85         1.18 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
        9.90        37.97         8.55        36.85        39.62         9.50 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC 
        8.09         9.99         2.43        11.31        36.30        34.29 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS 
       17.98        19.43        16.01        35.54         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       34.98         9.53        29.46         2.73        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      125.65       111.91        56.02        25.08        21.60        60.49 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       13.81        12.72        22.92        16.14        27.35        18.41 
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-A19H TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE 
       34.88        42.84         9.57        36.07        78.44         1.51 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 
       13.08        11.74         9.04         6.58        22.49         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
        5.36        13.28         2.20         3.29        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        17.33         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-RP-A693 TCGA-RP-A694 
        0.85        44.28        10.13        11.84         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8K5 
      164.19        60.03         2.99        10.98         5.49         6.48 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       21.07        13.12         3.42         1.08        19.96        12.07 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                           0.20                            0.13 
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                         185.16                          164.19 
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                          15.62                           13.81 
[1] "0.2 - 185.2 (15.6)" "0.1 - 164.2 (13.8)"
[1] "hr=" "1.1"
D21V2, survival
                                 sevent
clus2                              0  1
  AMP PEAK 21(20Q13.33) MUTATED   90 86
  AMP PEAK 21(20Q13.33) WILD-TYPE 83 80
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                            176                             163 
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                             86                              80 
$`AMP PEAK 21(20Q13.33) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 
       17.03        12.99        16.57       112.57        31.59        23.77 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53        86.76        11.87        62.07       113.52        42.08 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58        56.19        59.57        58.06       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K 
       60.23       103.59        39.75        45.30       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       63.81       135.75       137.92       178.32       125.19        79.59 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       11.61        58.52       170.20        89.13        95.24       137.79 
TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       29.06       151.53         6.41        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA 
       66.25        36.03        20.38       176.55        61.18        65.92 
TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
      215.44        54.02        17.29        12.20        27.22        94.98 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D 
       26.89        68.15       133.81       168.26        63.35        13.97 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W 
       63.78         2.60        56.42        14.47       369.93       195.02 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       17.92       102.90        39.29        86.14        59.28       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
      208.04        48.72        75.48        90.97       126.81        13.91 
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-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      103.20        16.96       248.65       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
      124.31       122.73        51.62         3.68        54.51        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH 
      172.18        36.95        64.08        53.19       201.80       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E 
      148.08        31.40        13.94         9.17        98.40        13.02 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19T 
      268.93         6.44       131.51        61.05       162.08         8.88 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-ER-A42K 
      148.18        43.82        23.34        31.27        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YD TCGA-FS-A1YX 
       92.98       174.21        15.72       210.08        29.46        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        28.08         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       40.27         9.70        47.38        23.93       101.26       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
      148.80        53.16        26.56        27.09        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
      174.84        77.88         0.20         7.23        11.74       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       84.72        64.44        62.79        32.48        39.58        12.62 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       50.10        21.37        59.41        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        6.67        18.05        63.02       219.16       105.04        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 
        8.61        90.28        52.34        22.68        43.73        10.36 
TCGA-YG-AA3O TCGA-YG-AA3P 
       36.03        14.43 

$`AMP PEAK 21(20Q13.33) WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       61.02        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-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF 
       12.10        66.08       130.72        46.98        46.32        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N 
       13.87         9.34       174.84        55.73        56.35        22.62 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
       26.89       125.79        18.18        30.84        15.19       228.99 
TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 
      161.00       129.63       117.17        54.67         3.65        18.12 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       11.34        11.11        22.95        48.89       117.21       194.83 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       107.34        53.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       10.49        15.68        13.87        10.16        17.85        68.25 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       52.01         6.35        29.82         8.65        33.73        14.70 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
        4.96       151.27        91.56        13.55        80.61        47.84 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S 
       72.07        64.64        56.84        18.61        37.35        55.92 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ 
       25.87        46.82        36.82        67.43       314.56        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MD 
       54.74        79.66        14.30        55.59        44.88        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       268.73       204.66        96.23       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AF TCGA-EE-A3AH 
      167.90        47.54        43.23       134.40        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A198 
      127.20        34.32        27.35        51.35        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19N 
       77.75        48.89        12.59        26.37       152.35        44.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       50.89        37.25        79.99        20.15        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      247.04        80.32        46.98        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB 
       34.82        94.39       216.92       228.59        20.91        48.85 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       15.45        32.75        74.73        11.41        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
       77.82        66.67        12.43        26.73        49.45        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       47.54         0.16        19.30         9.90         2.04       139.89 
TCGA-GN-A266 TCGA-GN-A4U8 TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
       10.13        46.36         0.33         0.69       212.22       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO 
        4.01        42.08        38.56        54.38        56.98        59.41 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S 
        3.75         2.20        30.18        15.16        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                           0.20                            0.16 
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                         369.93                          314.56 
  AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE 
                          57.24                           46.98 
[1] "0.2 - 369.9 (57.2)" "0.2 - 314.6 (47.0)"
[1] "hr=" "1.2"
D21V3, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 21(20Q13.33) MUTATED                   34             4
  AMP PEAK 21(20Q13.33) WILD-TYPE                 27             1
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 21(20Q13.33) MUTATED                                          33
  AMP PEAK 21(20Q13.33) WILD-TYPE                                        39
                                 vv
clus                              REGIONAL LYMPH NODE
  AMP PEAK 21(20Q13.33) MUTATED                   110
  AMP PEAK 21(20Q13.33) WILD-TYPE                  99
D21V4, multiclass
                                           clus
vv                                          AMP PEAK 21(20Q13.33) MUTATED
  DISTANT METASTASIS                                                   34
  PRIMARY TUMOR                                                         4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            33
  REGIONAL LYMPH NODE                                                 110
                                           clus
vv                                          AMP PEAK 21(20Q13.33) WILD-TYPE
  DISTANT METASTASIS                                                     27
  PRIMARY TUMOR                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                              39
  REGIONAL LYMPH NODE                                                    99
[1] 4 2
[1] 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(20Q13.33) MUTATED             9       3      18       10       17
  AMP PEAK 21(20Q13.33) WILD-TYPE           3       4      10        7       10
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 21(20Q13.33) MUTATED         10         6         5         9
  AMP PEAK 21(20Q13.33) WILD-TYPE       12         8        14         3
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 21(20Q13.33) MUTATED          21          9         20         26
  AMP PEAK 21(20Q13.33) WILD-TYPE        14          6         12         32
                                 vv
clus                              STAGE IV
  AMP PEAK 21(20Q13.33) MUTATED          5
  AMP PEAK 21(20Q13.33) WILD-TYPE       14
D21V5, multiclass
             clus
vv            AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE
  I OR II NOS                             9                               3
  STAGE 0                                 3                               4
  STAGE I                                18                              10
  STAGE IA                               10                               7
  STAGE IB                               17                              10
  STAGE II                               10                              12
  STAGE IIA                               6                               8
  STAGE IIB                               5                              14
  STAGE IIC                               9                               3
  STAGE III                              21                              14
  STAGE IIIA                              9                               6
  STAGE IIIB                             20                              12
  STAGE IIIC                             26                              32
  STAGE IV                                5                              14
[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(20Q13.33) MUTATED      37 43 31 37
  AMP PEAK 21(20Q13.33) WILD-TYPE    26 28 43 30
D21V6, multiclass
       clus
vv      AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE
  T0+T1                            37                              26
  T2                               43                              28
  T3                               31                              43
  T4                               37                              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 21(20Q13.33) MUTATED   90 36 17 23
  AMP PEAK 21(20Q13.33) WILD-TYPE 78 25 21 24
D21V7, multiclass
    clus
vv   AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE
  N0                            90                              78
  N1                            36                              25
  N2                            17                              21
  N3                            23                              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 21(20Q13.33) MUTATED   165   2   3   1   0
  AMP PEAK 21(20Q13.33) WILD-TYPE 141   2   0   3   9
D21V8, multiclass
     clus
vv    AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE
  M0                            165                             141
  M1                              2                               2
  M1A                             3                               0
  M1B                             1                               3
  M1C                             0                               9
[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(20Q13.33) MUTATED   74 41
  AMP PEAK 21(20Q13.33) WILD-TYPE 55 46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q13.33) MUTATED     74   41
  AMP PEAK 21(20Q13.33) WILD-TYPE   55   46
     clus
vv    AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE
  NO                             74                              55
  YES                            41                              46
[1] 2 2
[1] FALSE
D21V10, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20Q13.33) MUTATED    22 159
  AMP PEAK 21(20Q13.33) WILD-TYPE  21 145
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q13.33) MUTATED     22  159
  AMP PEAK 21(20Q13.33) WILD-TYPE   21  145
     clus
vv    AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE
  NO                             22                              21
  YES                           159                             145
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20Q13.33) MUTATED    68 114
  AMP PEAK 21(20Q13.33) WILD-TYPE  63 103
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q13.33) MUTATED     68  114
  AMP PEAK 21(20Q13.33) WILD-TYPE   63  103
        clus
vv       AMP PEAK 21(20Q13.33) MUTATED AMP PEAK 21(20Q13.33) WILD-TYPE
  FEMALE                            68                              63
  MALE                             114                             103
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(20Q13.33) MUTATED       2                         0   171
  AMP PEAK 21(20Q13.33) WILD-TYPE     3                         1   155
D21V13, multiclass
                           clus
vv                          AMP PEAK 21(20Q13.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               171
                           clus
vv                          AMP PEAK 21(20Q13.33) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                 155
[1] 3 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(20Q13.33) MUTATED     4 174
  AMP PEAK 21(20Q13.33) WILD-TYPE   3 160
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q13.33) MUTATED      4  174
  AMP PEAK 21(20Q13.33) WILD-TYPE    3  160
                        clus
vv                       AMP PEAK 21(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           174
                        clus
vv                       AMP PEAK 21(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             160
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(22Q13.2) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 22(22Q13.2) MUTATED   74 66
  AMP PEAK 22(22Q13.2) WILD-TYPE 94 99
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                           140                            193 
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                            66                             99 
$`AMP PEAK 22(22Q13.2) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB 
        6.97        16.47        22.55        85.32        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC 
       86.76        92.42        64.44        59.57        15.25        61.38 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51T TCGA-D3-A5GL 
       13.32         9.34        26.37        29.23        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GI 
       52.01        13.68        17.72        29.72        22.06         4.18 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
      142.45        75.65        11.44         4.01         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH 
       36.69        25.15         4.93        22.36        17.56         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
       23.15        19.00        13.35         0.20        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        8.12         5.13         9.21         1.08        39.62         9.50 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.09         8.84        32.15         8.09        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN 
       36.33        51.12        47.21        30.08        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2MN 
       55.69        98.27         2.70        29.46        63.42        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        60.49        53.16         5.56       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB 
        3.68        30.15        15.95        21.60        21.60         0.95 
TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
       27.35        25.18         3.78       114.15        13.45        28.60 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A3YN 
        6.58        17.72        13.08        12.62         6.58        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YY 
       85.74        15.72         6.71        13.28         4.70        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-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-QB-A6FS 
       12.16        14.70        14.50        14.50        15.81         5.79 
TCGA-QB-AA9O TCGA-RP-A694 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZY 
       18.05         0.69         5.49         6.48        18.67         5.36 
TCGA-WE-AAA3 TCGA-YG-AA3O 
        1.94         6.18 

$`AMP PEAK 22(22Q13.2) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         8.52       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      110.79        28.08        45.83        81.24        10.29         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       21.14        11.41        44.19         7.50        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
       56.19       114.67        46.98        46.32        82.29        24.00 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        6.31       103.59        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GD 
       32.28        21.44        32.61        47.87        23.11        10.22 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
       15.19       108.79        38.93       124.47        87.62         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I4 
       24.07        21.93         5.72        14.60        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       44.52         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.20        13.22        11.57         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.31        60.23         4.34        15.85         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        62.79         8.55        36.85 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         9.99        30.44         2.43        11.31        49.22 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.29        17.98        60.00        19.43        16.01        35.54 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53         2.73        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT 
       14.56       125.65       111.91        56.02        26.99        52.67 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       51.62        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        18.41        21.73        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-ER-A42K TCGA-FR-A7U8 TCGA-FR-A7U9 
        9.04        22.49         1.71         5.62         3.58         5.36 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        2.20         3.29        64.47         3.45        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       15.52         3.39        20.38        11.08        12.92        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        8.81         5.23        53.85        14.20        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 
        0.85        11.61        44.28        10.13        11.84        10.65 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
       14.50         0.43        11.05         0.33       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       60.03         2.99        10.98       185.16        71.01        11.84 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
        7.10        21.07        13.12         3.72         3.42        21.83 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        1.08        19.96        12.07         4.70         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                          0.13                           0.16 
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                        142.45                         185.16 
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                        16.355                         13.680 
[1] "0.1 - 142.4 (16.4)" "0.2 - 185.2 (13.7)"
[1] "hr=" "1.1"
D22V2, survival
                                sevent
clus2                             0  1
  AMP PEAK 22(22Q13.2) MUTATED   75 67
  AMP PEAK 22(22Q13.2) WILD-TYPE 98 99
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                           142                            197 
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                            67                             99 
$`AMP PEAK 22(22Q13.2) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB 
       12.99        16.57        31.59       103.10       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC 
       86.76       171.58        66.08        59.57        58.06        86.93 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51T TCGA-D3-A5GL 
       60.23         9.34        39.75        45.30        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GI 
      135.75       178.32        18.18        30.84        79.59        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z1 
      228.99        95.24        29.06       151.53         6.41        11.34 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        66.25        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       194.83        61.18        53.92        65.92        23.44 
TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 
      215.44        17.85        68.25        54.02        17.29        12.20 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L 
       27.22         8.65        94.98        68.15       168.26         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X 
       56.84        18.61        37.35        14.47       195.02        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI 
       36.82        39.29        86.14        59.28       208.04        48.72 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2ME 
       75.48        90.97       126.81       129.27        28.83       103.27 
TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       96.23        47.54        43.23       134.40       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 
      124.31       122.73         3.68        54.51        23.47        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G 
       64.08       201.80        27.35        98.40        48.89       268.93 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A2NG 
      131.51        61.05         8.88       148.18        16.37        31.27 
TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7UA 
       80.32        92.98       174.21        15.72       210.08        38.27 
TCGA-FR-A8YD TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE 
       29.46       228.59         7.79        27.72        53.52        40.27 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        9.70        32.75        23.93       101.26       133.55       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 
       53.16        26.56        49.48        27.09        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 
       28.73        77.88         0.20        47.54       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A8LL 
       64.44        62.79        32.48        39.58        50.10        21.37 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-WE-A8K1 TCGA-WE-A8K5 
       65.88         6.67        18.05         0.69        38.56        54.38 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YG-AA3O 
       90.28        43.73        10.36        36.03 

$`AMP PEAK 22(22Q13.2) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      133.25        28.08        90.90        95.74        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
       56.19       130.72        46.98        46.32       166.52        24.53 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       13.87       103.59       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GD 
       32.94        22.62        63.81       137.92       125.19        11.61 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
       15.19       170.20        89.13       161.00       137.79       129.63 
TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      117.17        54.67         3.65        18.12        22.29        11.11 
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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        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        63.78        72.07        64.64        56.42        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD 
      369.93        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 
      161.03        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       47.28       268.73       103.20        16.96       204.66       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF 
      203.05       167.90       248.65        71.21        51.62        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      138.81       172.18       127.20        34.32        53.19        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       148.08        31.40        35.44        13.94        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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 
        6.44        44.05       162.08        50.89        37.25        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       43.82        23.34        20.15        32.05       247.04        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YE 
       33.21         6.77        15.16         7.00        34.82        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB 
      216.92        48.59       202.65        20.91        28.08        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZZ 
      357.37        15.45        47.38        74.73        11.41        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
       77.82       174.84        12.43        26.73        49.45        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-LH-A9QB 
      139.89        10.13        46.36        12.62        59.41       357.04 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
      294.77         0.33       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZN 
       42.08       219.16       105.04        24.03         8.61        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 
       59.41        52.34         3.75        22.68         2.20        30.18 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        14.43        23.64        93.07        11.74 

  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                          0.20                           0.16 
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                        268.93                         369.93 
  AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE 
                         53.39                          48.59 
[1] "0.2 - 268.9 (53.4)" "0.2 - 369.9 (48.6)"
[1] "hr=" "1.1"
D22V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 22(22Q13.2) MUTATED                   22             5
  AMP PEAK 22(22Q13.2) WILD-TYPE                 39             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  AMP PEAK 22(22Q13.2) MUTATED                                          33
  AMP PEAK 22(22Q13.2) WILD-TYPE                                        39
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 22(22Q13.2) MUTATED                    85
  AMP PEAK 22(22Q13.2) WILD-TYPE                 124
D22V4, multiclass
                                           clus
vv                                          AMP PEAK 22(22Q13.2) MUTATED
  DISTANT METASTASIS                                                  22
  PRIMARY TUMOR                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           33
  REGIONAL LYMPH NODE                                                 85
                                           clus
vv                                          AMP PEAK 22(22Q13.2) WILD-TYPE
  DISTANT METASTASIS                                                    39
  PRIMARY TUMOR                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             39
  REGIONAL LYMPH NODE                                                  124
[1] 4 2
[1] 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(22Q13.2) MUTATED             4       3      11        5       11
  AMP PEAK 22(22Q13.2) WILD-TYPE           8       4      17       12       16
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 22(22Q13.2) MUTATED          7         5         5         8
  AMP PEAK 22(22Q13.2) WILD-TYPE       15         9        14         4
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 22(22Q13.2) MUTATED          18          9         13         27
  AMP PEAK 22(22Q13.2) WILD-TYPE        17          6         19         31
                                vv
clus                             STAGE IV
  AMP PEAK 22(22Q13.2) MUTATED          7
  AMP PEAK 22(22Q13.2) WILD-TYPE       12
D22V5, multiclass
             clus
vv            AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE
  I OR II NOS                            4                              8
  STAGE 0                                3                              4
  STAGE I                               11                             17
  STAGE IA                               5                             12
  STAGE IB                              11                             16
  STAGE II                               7                             15
  STAGE IIA                              5                              9
  STAGE IIB                              5                             14
  STAGE IIC                              8                              4
  STAGE III                             18                             17
  STAGE IIIA                             9                              6
  STAGE IIIB                            13                             19
  STAGE IIIC                            27                             31
  STAGE IV                               7                             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 22(22Q13.2) MUTATED      26 35 26 30
  AMP PEAK 22(22Q13.2) WILD-TYPE    37 36 48 37
D22V6, multiclass
       clus
vv      AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE
  T0+T1                           26                             37
  T2                              35                             36
  T3                              26                             48
  T4                              30                             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 22(22Q13.2) MUTATED    61  28  19  23
  AMP PEAK 22(22Q13.2) WILD-TYPE 107  33  19  24
D22V7, multiclass
    clus
vv   AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE
  N0                           61                            107
  N1                           28                             33
  N2                           19                             19
  N3                           23                             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 22(22Q13.2) MUTATED   126   1   2   1   4
  AMP PEAK 22(22Q13.2) WILD-TYPE 180   3   1   3   5
D22V8, multiclass
     clus
vv    AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE
  M0                           126                            180
  M1                             1                              3
  M1A                            2                              1
  M1B                            1                              3
  M1C                            4                              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(22Q13.2) MUTATED   55 41
  AMP PEAK 22(22Q13.2) WILD-TYPE 74 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(22Q13.2) MUTATED     55   41
  AMP PEAK 22(22Q13.2) WILD-TYPE   74   46
     clus
vv    AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE
  NO                            55                             74
  YES                           41                             46
[1] 2 2
[1] FALSE
D22V10, binary
                                cls
clus                               0   1
  AMP PEAK 22(22Q13.2) MUTATED    18 127
  AMP PEAK 22(22Q13.2) WILD-TYPE  25 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(22Q13.2) MUTATED     18  127
  AMP PEAK 22(22Q13.2) WILD-TYPE   25  177
     clus
vv    AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE
  NO                            18                             25
  YES                          127                            177
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, binary
                                cls
clus                               0   1
  AMP PEAK 22(22Q13.2) MUTATED    57  88
  AMP PEAK 22(22Q13.2) WILD-TYPE  74 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(22Q13.2) MUTATED     57   88
  AMP PEAK 22(22Q13.2) WILD-TYPE   74  129
        clus
vv       AMP PEAK 22(22Q13.2) MUTATED AMP PEAK 22(22Q13.2) WILD-TYPE
  FEMALE                           57                             74
  MALE                             88                            129
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(22Q13.2) MUTATED       3                         1   136
  AMP PEAK 22(22Q13.2) WILD-TYPE     2                         0   190
D22V13, multiclass
                           clus
vv                          AMP PEAK 22(22Q13.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              136
                           clus
vv                          AMP PEAK 22(22Q13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                190
[1] 3 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(22Q13.2) MUTATED     1 141
  AMP PEAK 22(22Q13.2) WILD-TYPE   6 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(22Q13.2) MUTATED      1  141
  AMP PEAK 22(22Q13.2) WILD-TYPE    6  193
                        clus
vv                       AMP PEAK 22(22Q13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          141
                        clus
vv                       AMP PEAK 22(22Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            193
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    42  35
  DEL PEAK  1(1P36.31) WILD-TYPE 126 130
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            77                            256 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            35                            130 
$`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-D3-A8GL TCGA-D3-A8GM 
       29.23        52.01        13.68        17.72        38.93        75.65 
TCGA-D9-A4Z6 TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 
        5.72        10.03        13.68        36.69        17.56        14.83 
TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A20H 
       19.00        10.55         8.12         1.35        15.85         9.21 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        9.90        11.15         8.84        60.00        47.21        30.08 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MK 
       55.69         1.15         8.84         9.53         7.96       125.65 
TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3JA 
       53.16       122.73         3.68        13.81         3.22        22.22 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE 
        3.78         3.52       114.15        36.07         1.87         1.51 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 
       11.74        22.49         1.71         5.62        15.72         3.58 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZJ 
       64.47         3.45        11.01        23.80         7.33        12.92 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD 
       40.64        27.39         0.82        14.20         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A26D TCGA-WE-A8K5 TCGA-WE-A8K6 
        0.20         0.13         0.16        14.70         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3P 
       18.67         1.08        19.96         1.94         4.70 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         6.97         8.52        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.79        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       11.41        44.19         7.50        36.16        92.42        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       59.57       114.67        46.98        46.32        82.29        61.38 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       24.00         6.31         9.34       103.59        26.37        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       25.78       110.24        47.87        23.11        29.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN 
       10.22        15.19         4.18       142.45       108.79       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
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-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
       51.12        39.19         9.99        44.52        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R 
       22.36         6.64        19.36         7.00        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13        23.15        13.35        13.22         0.20        11.57 
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        60.23 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        4.34         1.18         7.99        37.97        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       17.98        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        5.42        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
        6.18        47.51        29.46         2.73        44.25        14.56 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       63.42       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
       60.49        52.67         5.56       124.31        51.62        30.15 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72        22.92        21.60        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57         6.58        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN 
       11.80        13.08        12.62         9.04         6.58        18.41 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       85.74         6.71         5.36        13.28         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
        3.29        14.24        15.52         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
        8.22        19.53        11.08         7.17        30.87        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       47.38        52.08         8.65         8.81        49.15         8.68 
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-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        5.98         0.99        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       15.42        12.16        11.84        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        15.81         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZN 
       10.98       185.16        71.01        11.84         5.49        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       13.12         3.72         3.42        21.83         5.36        12.07 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         8.22         6.67         5.98 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        125.65                         185.16 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        12.920                         16.075 
[1] "0.1 - 125.7 (12.9)" "0.1 - 185.2 (16.1)"
[1] "hr=" "1.1"
D23V2, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    42  36
  DEL PEAK  1(1P36.31) WILD-TYPE 131 130
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            78                            261 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            36                            130 
$`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-D3-A8GL TCGA-D3-A8GM 
       45.30       135.75       178.32        18.18        89.13        95.24 
TCGA-D9-A1JX TCGA-D9-A4Z6 TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 
        6.41        11.11        20.38       176.55        61.18       215.44 
TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20F 
       15.68        54.02        27.22        94.98        14.70        91.56 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A2GE TCGA-EE-A2GH 
      168.26        80.61        13.97        14.47       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MH 
       48.72       126.81        14.30        21.67        47.28        16.96 
TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
      158.63       162.48       122.73         3.68        13.81       172.18 
TCGA-EE-A3JA TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19S TCGA-ER-A2ND 
       53.19        48.89        12.59       268.93        37.25        23.34 
TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P 
       20.15        32.05        46.98        33.21         6.77        15.72 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z7 
       15.16       216.92        48.59       228.59       202.65         7.79 
TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F8 TCGA-FS-A4FC 
       47.38        53.16        49.48        27.09       174.84        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A26D TCGA-WE-A8K5 
       77.88         0.20        47.54         0.16        39.58        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3P 
        8.61        90.28         2.20        30.18        10.36        14.43 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.67       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87        62.07       113.52        42.08       171.58        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       59.57       130.72        46.98        46.32       166.52        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       24.53        13.87         9.34       103.59        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       26.89       125.79       137.92       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN 
       11.61        15.19        58.52       228.99       170.20       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      137.79        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65        18.12        11.34        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       66.25        22.95        48.89        36.03       117.21       194.83 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       28.60        10.49        13.87        10.16        17.85        68.25 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       17.29        52.01         6.35        12.20        29.82         8.65 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        47.84        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        2.60        56.84        18.61        56.42        37.35        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       89.33        54.74        79.66        75.48        90.97        13.91 
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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51       103.27       268.73       103.20       204.66        96.23 
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       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG 
       71.21        53.26       124.31        51.62        54.51        23.47 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
      138.81       127.20        36.95        64.08        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18        79.99        43.82 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A 
       16.37        31.27       247.04        80.32        92.98       174.21 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      210.08         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91        28.08        27.72        48.85       357.37        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-A1ZZ 
       74.73       133.55        11.41       148.80        26.56        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-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       22.92        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       32.48        46.36        12.62        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       212.22        63.02       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      219.16       105.04        24.03        38.56        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-YG-AA3O 
       52.34         3.75        22.68        43.73        15.16        36.03 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.16                           0.33 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        268.93                         369.93 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         47.46                          52.34 
[1] "0.2 - 268.9 (47.5)" "0.3 - 369.9 (52.3)"
[1] "hr=" "1"  
D23V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  1(1P36.31) MUTATED                   17             0
  DEL PEAK  1(1P36.31) WILD-TYPE                 44             5
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  1(1P36.31) MUTATED                                          15
  DEL PEAK  1(1P36.31) WILD-TYPE                                        57
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK  1(1P36.31) MUTATED                    48
  DEL PEAK  1(1P36.31) WILD-TYPE                 161
D23V4, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.31) MUTATED
  DISTANT METASTASIS                                                  17
  PRIMARY TUMOR                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           15
  REGIONAL LYMPH NODE                                                 48
                                           clus
vv                                          DEL PEAK  1(1P36.31) WILD-TYPE
  DISTANT METASTASIS                                                    44
  PRIMARY TUMOR                                                          5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             57
  REGIONAL LYMPH NODE                                                  161
[1] 4 2
[1] 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        3        5
  DEL PEAK  1(1P36.31) WILD-TYPE          11       6      18       14       22
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  1(1P36.31) MUTATED          4         2         4         1
  DEL PEAK  1(1P36.31) WILD-TYPE       18        12        15        11
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  1(1P36.31) MUTATED          11          0          8         20
  DEL PEAK  1(1P36.31) WILD-TYPE        24         15         24         38
                                vv
clus                             STAGE IV
  DEL PEAK  1(1P36.31) MUTATED          5
  DEL PEAK  1(1P36.31) WILD-TYPE       14
D23V5, multiclass
             clus
vv            DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  I OR II NOS                            1                             11
  STAGE 0                                1                              6
  STAGE I                               10                             18
  STAGE IA                               3                             14
  STAGE IB                               5                             22
  STAGE II                               4                             18
  STAGE IIA                              2                             12
  STAGE IIB                              4                             15
  STAGE IIC                              1                             11
  STAGE III                             11                             24
  STAGE IIIA                             0                             15
  STAGE IIIB                             8                             24
  STAGE IIIC                            20                             38
  STAGE IV                               5                             14
[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      18 21 13 17
  DEL PEAK  1(1P36.31) WILD-TYPE    45 50 61 50
D23V6, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T0+T1                           18                             45
  T2                              21                             50
  T3                              13                             61
  T4                              17                             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
  DEL PEAK  1(1P36.31) MUTATED    38  16   8  13
  DEL PEAK  1(1P36.31) WILD-TYPE 130  45  30  34
D23V7, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                           38                            130
  N1                           16                             45
  N2                            8                             30
  N3                           13                             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  1(1P36.31) MUTATED    70   1   2   0   2
  DEL PEAK  1(1P36.31) WILD-TYPE 236   3   1   4   7
D23V8, multiclass
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  M0                            70                            236
  M1                             1                              3
  M1A                            2                              1
  M1B                            0                              4
  M1C                            2                              7
[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
  DEL PEAK  1(1P36.31) MUTATED   31 21
  DEL PEAK  1(1P36.31) WILD-TYPE 98 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     31   21
  DEL PEAK  1(1P36.31) WILD-TYPE   98   66
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                            31                             98
  YES                           21                             66
[1] 2 2
[1] FALSE
D23V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     9  70
  DEL PEAK  1(1P36.31) WILD-TYPE  34 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      9   70
  DEL PEAK  1(1P36.31) WILD-TYPE   34  234
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                             9                             34
  YES                           70                            234
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    34  46
  DEL PEAK  1(1P36.31) WILD-TYPE  97 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     34   46
  DEL PEAK  1(1P36.31) WILD-TYPE   97  171
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           34                             97
  MALE                             46                            171
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED       1                         0    74
  DEL PEAK  1(1P36.31) WILD-TYPE     4                         1   252
D23V13, multiclass
                           clus
vv                          DEL PEAK  1(1P36.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               74
                           clus
vv                          DEL PEAK  1(1P36.31) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                252
[1] 3 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
  DEL PEAK  1(1P36.31) MUTATED     1  78
  DEL PEAK  1(1P36.31) WILD-TYPE   6 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1   78
  DEL PEAK  1(1P36.31) WILD-TYPE    6  256
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            256
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  2(1P22.1) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P22.1) MUTATED    46  43
  DEL PEAK  2(1P22.1) WILD-TYPE 122 122
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           89                           244 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           43                           122 
$`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        86.76 
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-D3-A8GB TCGA-D3-A8GR 
       29.23        52.01        13.68        17.72        29.72         5.56 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 
       21.93         5.72        10.03        13.68        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL 
        4.93        17.56        14.83         0.20        19.00        13.35 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D 
       10.55         8.12        60.23         9.21        37.97        11.15 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GO TCGA-EE-A2GR 
        8.84        30.44        34.29        60.00        55.69         1.15 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH 
      125.65        26.99        53.16       122.73         3.68        12.72 
TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
        3.22        31.40        12.95         3.78         3.52        13.45 
TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
       28.60        36.07         6.58         1.87        12.62        11.74 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1Z0 
       22.49         1.71         5.62        15.72         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 TCGA-GN-A8LK TCGA-GN-A8LL 
        0.16        44.28        14.70        10.65        14.50        14.50 
TCGA-HR-A2OH TCGA-QB-AA9O TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZM 
       15.81        18.05         8.98        11.84         6.48        18.67 
TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3P TCGA-Z2-A8RT 
        3.72         1.08         1.94         4.70         8.22 

$`DEL PEAK  2(1P22.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
        3.02         6.97         6.97        16.47         8.52        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
       70.16       110.79        45.83        81.24         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       88.50        68.22        44.19         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       92.42        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       82.29        24.00         6.31       103.59        26.37        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       25.78       110.24        47.87        23.11        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A6E9 
      124.47        87.62        11.44        24.07         4.01         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-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       39.19         9.99        44.52        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
        7.00        13.15         0.13        23.15        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57         6.31         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.31         4.34        15.85         1.18         7.99         9.90 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       62.79         8.55        36.85         1.08        39.62         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       12.03         8.09         9.99         2.43        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        47.21        30.08        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-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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         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        60.49        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
        5.56       124.31        51.62        30.15        13.81        15.95 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       27.35        18.41        21.73        33.60        18.61        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        5.72        76.41        25.18        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       34.88         4.21        42.84        34.68         9.57        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       78.44        11.80         1.51        13.08         9.04         6.58 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       18.41        85.74         6.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        2.20         4.70         3.29        64.47        11.01        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.30         3.39        20.38         8.22        19.53 
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-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
        8.65         8.81         8.68         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        3.22         7.36        28.73        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.99         0.13        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23         0.85        11.61        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB 
       16.24        15.42        12.16        11.84        14.50         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
       11.05         5.79         0.33         0.69       164.19        60.03 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
        2.99        10.98       185.16        71.01         5.49         7.10 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 
       21.07        13.12         3.42        21.83         5.36        19.96 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         6.67         5.98 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                         0.16                          0.13 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       125.65                        185.16 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                        14.20                         15.47 
[1] "0.2 - 125.7 (14.2)" "0.1 - 185.2 (15.5)"
[1] "hr=" "1"  
D24V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P22.1) MUTATED    46  43
  DEL PEAK  2(1P22.1) WILD-TYPE 127 123
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           89                           250 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           43                           123 
$`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        86.76 
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-D3-A8GB TCGA-D3-A8GR 
       45.30       135.75       178.32        18.18        30.84       129.63 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 
       22.29        11.11        20.38       176.55        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        54.02        17.29 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D 
       27.22        94.98       133.81       168.26        47.84        13.97 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GO TCGA-EE-A2GR 
       14.47       369.93        67.43       161.03       126.81        14.30 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH 
      158.63       248.65       162.48       122.73         3.68       138.81 
TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
      172.18        31.40        13.94        48.89        12.59       131.51 
TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
       61.05        37.25         8.88        23.34        31.27        32.05 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1Z0 
       46.98        33.21         6.77        15.72        48.59       202.65 
TCGA-FS-A1Z7 TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 
        7.79        47.38       148.80        53.16        49.48       174.84 
TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
        0.16       139.89        39.58        12.62        50.10        21.37 
TCGA-HR-A2OH TCGA-QB-AA9O TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZM 
       65.88        18.05        63.02        24.03        54.38        90.28 
TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3P TCGA-Z2-A8RT 
       52.34         2.20        10.36        14.43        23.64 

$`DEL PEAK  2(1P22.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.57        16.67       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
       71.80       133.25        90.90        95.74        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      115.53       168.00        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
      166.52        24.53        13.87       103.59        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       26.89       125.79       137.92       125.19        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      161.00       137.79        29.06       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        18.12        11.34         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       66.25        22.95        48.89        36.03       117.21       194.83 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       35.93       107.34        23.44        68.09        28.60        10.49 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        17.85        68.25        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82         8.65        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.96       151.27        91.56        13.55        63.35        80.61 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       63.78        72.07        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        37.35        55.92        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       75.48        90.97        13.91        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      203.05       167.90        47.54        43.23       134.40        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       124.31        51.62        54.51        13.81        23.47 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       109.58       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-FR-A7UA 
       92.98       174.21       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       34.82        29.46        94.39       216.92       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        32.75        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      133.55        11.41        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-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        22.92        47.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23         2.04        11.74       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB 
       64.44        62.79        32.48        46.36        59.41       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
      294.77         6.67         0.33         0.69       212.22       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
        4.01        42.08       219.16       105.04        38.56         8.61 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 
       56.98        59.41         3.75        22.68        43.73        30.18 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        93.07        11.74 

  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 
                       369.93                        357.37 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       48.590                        51.485 
[1] "0.2 - 369.9 (48.6)" "0.2 - 357.4 (51.5)"
[1] "hr=" "1"  
D24V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  2(1P22.1) MUTATED                   13             1
  DEL PEAK  2(1P22.1) WILD-TYPE                 48             4
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  2(1P22.1) MUTATED                                          19
  DEL PEAK  2(1P22.1) WILD-TYPE                                        53
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  2(1P22.1) MUTATED                    57
  DEL PEAK  2(1P22.1) WILD-TYPE                 152
D24V4, multiclass
                                           clus
vv                                          DEL PEAK  2(1P22.1) MUTATED
  DISTANT METASTASIS                                                 13
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          19
  REGIONAL LYMPH NODE                                                57
                                           clus
vv                                          DEL PEAK  2(1P22.1) WILD-TYPE
  DISTANT METASTASIS                                                   48
  PRIMARY TUMOR                                                         4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            53
  REGIONAL LYMPH NODE                                                 152
[1] 4 2
[1] 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             1       1       9        1        5
  DEL PEAK  2(1P22.1) WILD-TYPE          11       6      19       16       22
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  2(1P22.1) MUTATED          6         1         5         3
  DEL PEAK  2(1P22.1) WILD-TYPE       16        13        14         9
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  2(1P22.1) MUTATED          14          0         14         20
  DEL PEAK  2(1P22.1) WILD-TYPE        21         15         18         38
                               vv
clus                            STAGE IV
  DEL PEAK  2(1P22.1) MUTATED          6
  DEL PEAK  2(1P22.1) WILD-TYPE       13
D24V5, multiclass
             clus
vv            DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  I OR II NOS                           1                            11
  STAGE 0                               1                             6
  STAGE I                               9                            19
  STAGE IA                              1                            16
  STAGE IB                              5                            22
  STAGE II                              6                            16
  STAGE IIA                             1                            13
  STAGE IIB                             5                            14
  STAGE IIC                             3                             9
  STAGE III                            14                            21
  STAGE IIIA                            0                            15
  STAGE IIIB                           14                            18
  STAGE IIIC                           20                            38
  STAGE IV                              6                            13
[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      16 21 20 21
  DEL PEAK  2(1P22.1) WILD-TYPE    47 50 54 46
D24V6, multiclass
       clus
vv      DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  T0+T1                          16                            47
  T2                             21                            50
  T3                             20                            54
  T4                             21                            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  2(1P22.1) MUTATED    34  22  12  15
  DEL PEAK  2(1P22.1) WILD-TYPE 134  39  26  32
D24V7, multiclass
    clus
vv   DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  N0                          34                           134
  N1                          22                            39
  N2                          12                            26
  N3                          15                            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  2(1P22.1) MUTATED    78   0   3   1   2
  DEL PEAK  2(1P22.1) WILD-TYPE 228   4   0   3   7
D24V8, multiclass
     clus
vv    DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  M0                           78                           228
  M1                            0                             4
  M1A                           3                             0
  M1B                           1                             3
  M1C                           2                             7
[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  2(1P22.1) MUTATED    28  29
  DEL PEAK  2(1P22.1) WILD-TYPE 101  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     28   29
  DEL PEAK  2(1P22.1) WILD-TYPE  101   58
     clus
vv    DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  NO                           28                           101
  YES                          29                            58
[1] 2 2
[1] FALSE
D24V10, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED    10  80
  DEL PEAK  2(1P22.1) WILD-TYPE  33 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     10   80
  DEL PEAK  2(1P22.1) WILD-TYPE   33  224
     clus
vv    DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  NO                           10                            33
  YES                          80                           224
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED    41  50
  DEL PEAK  2(1P22.1) WILD-TYPE  90 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     41   50
  DEL PEAK  2(1P22.1) WILD-TYPE   90  167
        clus
vv       DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  FEMALE                          41                            90
  MALE                            50                           167
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P22.1) MUTATED       2                         0    82
  DEL PEAK  2(1P22.1) WILD-TYPE     3                         1   244
D24V13, multiclass
                           clus
vv                          DEL PEAK  2(1P22.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              82
                           clus
vv                          DEL PEAK  2(1P22.1) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               244
[1] 3 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  2(1P22.1) MUTATED     2  86
  DEL PEAK  2(1P22.1) WILD-TYPE   5 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED      2   86
  DEL PEAK  2(1P22.1) WILD-TYPE    5  248
                        clus
vv                       DEL PEAK  2(1P22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          86
                        clus
vv                       DEL PEAK  2(1P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           248
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  3(2Q37.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q37.3) MUTATED    36  46
  DEL PEAK  3(2Q37.3) WILD-TYPE 132 119
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           82                           251 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           46                           119 
$`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        86.76        11.41         7.50         6.31        15.25 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A8GD 
       82.29       103.59        26.37        32.28        25.78        10.22 
TCGA-D3-A8GM TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-DA-A1IA TCGA-EB-A44R TCGA-EE-A180 
       75.65        11.31        10.03         4.93         0.20         8.12 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C 
       60.23         4.34        15.85         9.21         1.18        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2GC TCGA-EE-A2GH 
       11.15        62.79        12.03         8.09        34.29        47.21 
TCGA-EE-A2GR TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AF 
        1.15         7.96        63.42       125.65        53.16        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 
       15.95         3.22        22.22        18.41        33.60        31.40 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND 
       12.95         3.78        34.68         6.58        17.72         1.87 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A8YC TCGA-FS-A1YW 
        6.58        22.49         1.71        85.74         2.20        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        3.45        11.01        23.80        12.92        47.38         8.65 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 
        5.23        53.85         7.36         0.20         0.13        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A8LL TCGA-HR-A2OH TCGA-W3-A824 
       10.13        16.24        14.70        14.50        15.81       164.19 
TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y 
       60.03        71.01         6.48        18.67         5.36         1.08 
TCGA-WE-AAA0 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       19.96         6.18         4.70         6.67 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
       32.42        70.16       110.79        28.08        22.55        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       10.29        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       44.19        36.16        92.42        56.19        64.44        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      114.67        46.98        46.32        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        6.31         9.34        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       54.31        21.44        32.61       110.24        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE 
       13.68        17.72        23.11        29.72        22.06        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
        4.18       142.45       108.79        38.93       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       11.44         5.56        24.07         4.01        21.93         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        13.22        14.60        48.79        35.80        51.12 
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-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-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.15         0.13        23.15        19.00        13.35        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20        11.57        10.55         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
       12.20         5.13         4.31         7.99         9.90         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       36.85         1.08        39.62         9.50         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       30.44         2.43        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       36.30         9.67        36.33        51.12        17.98        60.00 
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 
       55.69         5.42        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        2.73        44.25        14.56       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        60.49        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 
      122.73        51.62         3.68        30.15        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH 
       21.60        21.60        16.14         0.95        27.35        21.73 
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-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
       28.60        42.84         9.57        36.07        78.44        11.80 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K 
        1.51        13.08        12.62        11.74         9.04         5.62 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       18.41        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        4.70         3.29        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-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       84.72        15.42        12.16        11.84        10.65        14.50 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       14.50         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ 
        0.69         8.98         2.99        10.98       185.16        11.84 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        5.49         7.10        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3V 
       21.83         1.94        12.07         8.22         5.98 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                         0.13                          0.13 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       164.19                        185.16 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       14.155                        15.190 
[1] "0.1 - 164.2 (14.2)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.3"
D25V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q37.3) MUTATED    39  46
  DEL PEAK  3(2Q37.3) WILD-TYPE 134 120
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           85                           254 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           46                           120 
$`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        86.76        11.87       113.52        12.10        58.06 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A8GD 
      166.52       103.59        39.75        32.94        26.89        11.61 
TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-DA-A1I0 
       95.24       151.53        54.67        18.12        25.18        20.38 
TCGA-DA-A1IA TCGA-EB-A44R TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       65.92        10.16        94.98       133.81       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P 
      168.26        13.55        47.84        13.97        63.78        56.42 
TCGA-EE-A29Q TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MH TCGA-EE-A2MJ 
       37.35        67.43       208.04        14.30        16.96        96.23 
TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JA 
      158.63       162.48        13.81        23.47       172.18        53.19 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19P 
       51.35       148.08        31.40        13.94        48.89       162.08 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
        8.88       148.18        23.34        80.32        46.98        33.21 
TCGA-FR-A44A TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        34.82       216.92        48.59       228.59       202.65 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       47.38       101.26       133.55        27.02        77.82        66.67 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D 
        0.20        47.54       117.93        10.13        64.44        39.58 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-A8K5 
       21.37        65.88       212.22       121.08       105.04        54.38 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3O TCGA-YG-AA3P 
       90.28        43.73         2.20        30.18        36.03        14.43 
TCGA-Z2-AA3S 
       93.07 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        31.59        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       62.07        42.08       171.58        56.19        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        46.98        46.32        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.87         9.34        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
      145.12        22.62        63.81       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE 
      178.32        18.18       125.19        30.84        79.59        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       58.52       228.99       170.20        89.13       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       29.06       129.63       117.17         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        11.11         9.90        66.25        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-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        53.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        17.85        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         6.35        12.20        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       63.35        80.61        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       18.61        14.47        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28       314.56       161.03        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       79.66        75.48        90.97       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73       103.20       204.66 
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       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
      201.80        27.35       109.58        35.44        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       77.75        98.40        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       37.25        79.99        43.82        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 
       32.05       247.04         6.77        92.98        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1Z3 
       15.16         7.00        38.27        29.46        94.39        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-A1ZK TCGA-FS-A1ZP 
       40.27        15.45         9.70        32.75        23.93        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-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-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       77.88        22.92         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
        2.04        11.74       139.89        84.72        62.79        32.48 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       46.36        12.62        50.10        59.41       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA1O 
        6.67        18.05         0.33         0.69        63.02         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN 
       42.08       219.16        24.03        38.56         8.61        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-WE-AAA4 
       59.41        52.34         3.75        22.68        10.36        15.16 
TCGA-Z2-A8RT TCGA-Z2-AA3V 
       23.64        11.74 

  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                        369.93 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        54.67                         49.17 
[1] "0.2 - 228.6 (54.7)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1.1"
D25V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  3(2Q37.3) MUTATED                   19             2
  DEL PEAK  3(2Q37.3) WILD-TYPE                 42             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  3(2Q37.3) MUTATED                                          22
  DEL PEAK  3(2Q37.3) WILD-TYPE                                        50
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  3(2Q37.3) MUTATED                    45
  DEL PEAK  3(2Q37.3) WILD-TYPE                 164
D25V4, multiclass
                                           clus
vv                                          DEL PEAK  3(2Q37.3) MUTATED
  DISTANT METASTASIS                                                 19
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          22
  REGIONAL LYMPH NODE                                                45
                                           clus
vv                                          DEL PEAK  3(2Q37.3) WILD-TYPE
  DISTANT METASTASIS                                                   42
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            50
  REGIONAL LYMPH NODE                                                 164
[1] 4 2
[1] 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             3       1       9        3        6
  DEL PEAK  3(2Q37.3) WILD-TYPE           9       6      19       14       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  3(2Q37.3) MUTATED          5         3         8         3
  DEL PEAK  3(2Q37.3) WILD-TYPE       17        11        11         9
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  3(2Q37.3) MUTATED           9          4          8          9
  DEL PEAK  3(2Q37.3) WILD-TYPE        26         11         24         49
                               vv
clus                            STAGE IV
  DEL PEAK  3(2Q37.3) MUTATED          7
  DEL PEAK  3(2Q37.3) WILD-TYPE       12
D25V5, multiclass
             clus
vv            DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  I OR II NOS                           3                             9
  STAGE 0                               1                             6
  STAGE I                               9                            19
  STAGE IA                              3                            14
  STAGE IB                              6                            21
  STAGE II                              5                            17
  STAGE IIA                             3                            11
  STAGE IIB                             8                            11
  STAGE IIC                             3                             9
  STAGE III                             9                            26
  STAGE IIIA                            4                            11
  STAGE IIIB                            8                            24
  STAGE IIIC                            9                            49
  STAGE IV                              7                            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
  DEL PEAK  3(2Q37.3) MUTATED      10 20 20 22
  DEL PEAK  3(2Q37.3) WILD-TYPE    53 51 54 45
D25V6, multiclass
       clus
vv      DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  T0+T1                          10                            53
  T2                             20                            51
  T3                             20                            54
  T4                             22                            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  3(2Q37.3) MUTATED    47  13   9   9
  DEL PEAK  3(2Q37.3) WILD-TYPE 121  48  29  38
D25V7, multiclass
    clus
vv   DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  N0                          47                           121
  N1                          13                            48
  N2                           9                            29
  N3                           9                            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                             M0  M1 M1A M1B M1C
  DEL PEAK  3(2Q37.3) MUTATED    72   1   3   1   3
  DEL PEAK  3(2Q37.3) WILD-TYPE 234   3   0   3   6
D25V8, multiclass
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  M0                           72                           234
  M1                            1                             3
  M1A                           3                             0
  M1B                           1                             3
  M1C                           3                             6
[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  3(2Q37.3) MUTATED   39 21
  DEL PEAK  3(2Q37.3) WILD-TYPE 90 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     39   21
  DEL PEAK  3(2Q37.3) WILD-TYPE   90   66
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  NO                           39                            90
  YES                          21                            66
[1] 2 2
[1] FALSE
D25V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED     6  83
  DEL PEAK  3(2Q37.3) WILD-TYPE  37 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      6   83
  DEL PEAK  3(2Q37.3) WILD-TYPE   37  221
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  NO                            6                            37
  YES                          83                           221
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q37.3) MUTATED    33  56
  DEL PEAK  3(2Q37.3) WILD-TYPE  98 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     33   56
  DEL PEAK  3(2Q37.3) WILD-TYPE   98  161
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  FEMALE                          33                            98
  MALE                            56                           161
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q37.3) MUTATED       1                         0    80
  DEL PEAK  3(2Q37.3) WILD-TYPE     4                         1   246
D25V13, multiclass
                           clus
vv                          DEL PEAK  3(2Q37.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              80
                           clus
vv                          DEL PEAK  3(2Q37.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               246
[1] 3 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  3(2Q37.3) MUTATED     5  81
  DEL PEAK  3(2Q37.3) WILD-TYPE   2 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      5   81
  DEL PEAK  3(2Q37.3) WILD-TYPE    2  253
                        clus
vv                       DEL PEAK  3(2Q37.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          81
                        clus
vv                       DEL PEAK  3(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           253
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  4(3P25.1) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(3P25.1) MUTATED    34  31
  DEL PEAK  4(3P25.1) WILD-TYPE 134 134
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           65                           268 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           31                           134 
$`DEL PEAK  4(3P25.1) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JN TCGA-D3-A3C6 
      111.09        32.42       110.79        85.32        56.19        15.25 
TCGA-D3-A3C7 TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D9-A6E9 
       46.98       110.24        23.11        29.72        87.62         9.90 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EB-A44R 
       11.31        35.80        13.68        44.52        36.69         0.20 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P 
       13.35        10.55         4.34        15.85         8.55        12.03 
TCGA-EE-A29V TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MF 
        2.43        47.21        98.27         2.70         9.53         2.73 
TCGA-EE-A2MH TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 
        7.96       124.31         3.22        21.60         0.95        18.61 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND 
       11.90        34.88        13.45         9.57        36.07         1.87 
TCGA-ER-A2NG TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FS-A1YX 
       12.62        85.74         6.71         5.36        13.28         3.45 
TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-FW-A3TV 
       15.52        47.38         8.65        14.20         0.13         0.16 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A4U9 TCGA-W3-AA1O 
        0.85        11.61        44.28        16.24        10.65         2.99 
TCGA-W3-AA21 TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
       71.01        21.83        12.07         4.70         6.67 

$`DEL PEAK  4(3P25.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       28.08        22.55        45.83        81.24        10.29         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        86.76        11.41        44.19 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
        7.50        36.16         6.31        92.42        64.44        59.57 
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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC 
       25.78        52.01        47.87        13.68        17.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       10.22        15.19         4.18       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
       75.65       124.47        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       21.93         5.72        13.22        14.60        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       10.03        39.19         9.99        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13        23.15        19.00        13.22         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         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        60.23         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15        62.79        36.85         1.08        39.62 
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        30.44        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       51.12        34.29        17.98        60.00        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        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
        1.15        13.02        34.98        36.33         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       47.51        29.46        44.25        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16        52.67         5.56       122.73        51.62         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-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        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-A19M 
        3.78         3.52        11.11       114.15         4.21        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84        34.68         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC 
        1.71         5.62        18.41        15.72         3.58         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.70         3.29        64.47        11.01        23.80        14.24 
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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        12.89        52.08 
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-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY 
        5.98         6.41         2.27         0.20         0.99        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        9.90         7.23        31.33        84.72        10.13        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       12.16        14.70        11.84        14.50        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       15.81         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W 
        0.69       164.19         8.98        60.03        10.98       185.16 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       11.84         5.49         6.48         7.10        18.67        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       13.12         3.72         3.42         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
        1.94         6.18         8.22         5.98 

  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                         0.13                          0.13 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                       124.31                        185.16 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                        13.35                         15.57 
[1] "0.1 - 124.3 (13.3)" "0.1 - 185.2 (15.6)"
[1] "hr=" "1"  
D26V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(3P25.1) MUTATED    35  31
  DEL PEAK  4(3P25.1) WILD-TYPE 138 135
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           66                           273 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           31                           135 
$`DEL PEAK  4(3P25.1) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JN TCGA-D3-A3C6 
      112.04       112.57       133.25       103.10        56.19        58.06 
TCGA-D3-A3C7 TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D9-A1X3 
       46.98       125.79       125.19        30.84       137.79        18.12 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
        9.90        25.18        36.03       176.55       107.34        61.18 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29G 
       10.16        17.29        27.22       151.27        91.56        72.07 
TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MD 
       56.42        25.87       208.04       129.27        28.83        47.28 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB 
      268.73        16.96       124.31       172.18        64.08       201.80 
TCGA-ER-A195 TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S 
       35.44        13.02       152.35       131.51        50.89        37.25 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA 
       23.34        31.27       174.21       210.08         7.00        38.27 
TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FW-A3TU 
       48.59        28.08       101.26       133.55       174.84        47.54 
TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A4U9 
        0.16         2.04        11.74       139.89        64.44        12.62 
TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
        4.01       105.04        22.68        15.16        14.43        93.07 

$`DEL PEAK  4(3P25.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       28.08        31.59        90.90        95.74        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        86.76        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10       171.58        66.08        59.57 
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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC 
       26.89       135.75       137.92       178.32        18.18        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       11.61        15.19        58.52       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       95.24       161.00        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65         6.41        11.34        22.29        11.11 
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-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       10.49       215.44        15.68        13.87        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       54.02        52.01         6.35        12.20        29.82         8.65 
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 
      133.81       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        64.64         2.60        56.84        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92       369.93       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       161.03        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       126.81        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-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20       204.66        96.23       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       122.73        51.62         3.68        54.51 
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-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        51.35       109.58       148.08        31.40 
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-A19M TCGA-ER-A19N 
       12.59        26.37       268.93         6.44        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      162.08         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD 
        6.77        92.98        15.72        15.16        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       94.39       216.92       228.59       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
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-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-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67        28.73        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45        77.88         0.20        22.92        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
        7.23       117.93        84.72        10.13        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       39.58        46.36        50.10        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      357.04       294.77         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ 
      212.22        63.02       121.08        42.08       219.16        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       38.56        54.38         8.61        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       52.34         3.75        43.73         2.20        30.18        10.36 
TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
       36.03        23.64        11.74 

  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                         0.16                          0.20 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                       268.73                        369.93 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                       56.305                        49.480 
[1] "0.2 - 268.7 (56.3)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D26V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  4(3P25.1) MUTATED                   10             2
  DEL PEAK  4(3P25.1) WILD-TYPE                 51             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  4(3P25.1) MUTATED                                          12
  DEL PEAK  4(3P25.1) WILD-TYPE                                        60
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  4(3P25.1) MUTATED                    43
  DEL PEAK  4(3P25.1) WILD-TYPE                 166
D26V4, multiclass
                                           clus
vv                                          DEL PEAK  4(3P25.1) MUTATED
  DISTANT METASTASIS                                                 10
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          12
  REGIONAL LYMPH NODE                                                43
                                           clus
vv                                          DEL PEAK  4(3P25.1) WILD-TYPE
  DISTANT METASTASIS                                                   51
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            60
  REGIONAL LYMPH NODE                                                 166
[1] 4 2
[1] 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(3P25.1) MUTATED             2       1      10        1        7
  DEL PEAK  4(3P25.1) WILD-TYPE          10       6      18       16       20
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  4(3P25.1) MUTATED          3         0         2         1
  DEL PEAK  4(3P25.1) WILD-TYPE       19        14        17        11
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  4(3P25.1) MUTATED          10          3          7         10
  DEL PEAK  4(3P25.1) WILD-TYPE        25         12         25         48
                               vv
clus                            STAGE IV
  DEL PEAK  4(3P25.1) MUTATED          1
  DEL PEAK  4(3P25.1) WILD-TYPE       18
D26V5, multiclass
             clus
vv            DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  I OR II NOS                           2                            10
  STAGE 0                               1                             6
  STAGE I                              10                            18
  STAGE IA                              1                            16
  STAGE IB                              7                            20
  STAGE II                              3                            19
  STAGE IIA                             0                            14
  STAGE IIB                             2                            17
  STAGE IIC                             1                            11
  STAGE III                            10                            25
  STAGE IIIA                            3                            12
  STAGE IIIB                            7                            25
  STAGE IIIC                           10                            48
  STAGE IV                              1                            18
[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(3P25.1) MUTATED      16 14 12  8
  DEL PEAK  4(3P25.1) WILD-TYPE    47 57 62 59
D26V6, multiclass
       clus
vv      DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  T0+T1                          16                            47
  T2                             14                            57
  T3                             12                            62
  T4                              8                            59
[1] 4 2
[1] 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(3P25.1) MUTATED    31  13  10   6
  DEL PEAK  4(3P25.1) WILD-TYPE 137  48  28  41
D26V7, multiclass
    clus
vv   DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  N0                          31                           137
  N1                          13                            48
  N2                          10                            28
  N3                           6                            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                             M0  M1 M1A M1B M1C
  DEL PEAK  4(3P25.1) MUTATED    59   0   0   0   1
  DEL PEAK  4(3P25.1) WILD-TYPE 247   4   3   4   8
D26V8, multiclass
     clus
vv    DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  M0                           59                           247
  M1                            0                             4
  M1A                           0                             3
  M1B                           0                             4
  M1C                           1                             8
[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  4(3P25.1) MUTATED    25  13
  DEL PEAK  4(3P25.1) WILD-TYPE 104  74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED     25   13
  DEL PEAK  4(3P25.1) WILD-TYPE  104   74
     clus
vv    DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  NO                           25                           104
  YES                          13                            74
[1] 2 2
[1] FALSE
D26V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P25.1) MUTATED     8  59
  DEL PEAK  4(3P25.1) WILD-TYPE  35 245
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED      8   59
  DEL PEAK  4(3P25.1) WILD-TYPE   35  245
     clus
vv    DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  NO                            8                            35
  YES                          59                           245
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P25.1) MUTATED    28  39
  DEL PEAK  4(3P25.1) WILD-TYPE 103 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED     28   39
  DEL PEAK  4(3P25.1) WILD-TYPE  103  178
        clus
vv       DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  FEMALE                          28                           103
  MALE                            39                           178
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3P25.1) MUTATED       2                         0    62
  DEL PEAK  4(3P25.1) WILD-TYPE     3                         1   264
D26V13, multiclass
                           clus
vv                          DEL PEAK  4(3P25.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              62
                           clus
vv                          DEL PEAK  4(3P25.1) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               264
[1] 3 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  4(3P25.1) MUTATED     1  65
  DEL PEAK  4(3P25.1) WILD-TYPE   6 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED      1   65
  DEL PEAK  4(3P25.1) WILD-TYPE    6  269
                        clus
vv                       DEL PEAK  4(3P25.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          65
                        clus
vv                       DEL PEAK  4(3P25.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           269
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  5(3Q13.31) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3Q13.31) MUTATED    25  30
  DEL PEAK  5(3Q13.31) WILD-TYPE 143 135
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            55                            278 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            30                            135 
$`DEL PEAK  5(3Q13.31) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GP 
       32.42       110.79         7.50        13.68        23.11        87.62 
TCGA-D3-A8GR TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
        5.56         9.90        11.31        13.68        44.52        36.69 
TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29G 
        0.20        10.55         8.12         4.34         1.18         8.55 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ 
       36.85        12.03         8.09        34.29        47.21        19.43 
TCGA-EE-A2GN TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A195 
       33.83        53.16        51.62         3.22        33.60        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A3EV TCGA-FR-A7U9 
       12.95        38.40        34.88        36.07        22.49         5.36 
TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A4F8 TCGA-FS-A4FD 
        2.20         3.45        12.92        47.38        14.20         2.27 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
        0.13        44.28        31.33        16.24        15.42        10.65 
TCGA-GN-A8LL TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P 
       14.50        10.98         5.49        21.83        12.07         4.70 
TCGA-Z2-AA3S 
        6.67 

$`DEL PEAK  5(3Q13.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.41        44.19        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       52.01        47.87        17.72        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      124.47        11.44        24.07         4.01        21.93         5.72 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       13.22        14.60        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       39.19         9.99        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       19.36         7.00        17.56        14.83        13.15         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       60.23        15.85         9.21         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       11.15        62.79         1.08        39.62         9.50         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 
        8.84         9.99        30.44         2.43        32.15        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       60.00        30.08        16.01        35.54        28.31        55.69 
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-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        60.49 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67         5.56       124.31       122.73         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        15.95        12.72        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       31.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90        11.11       114.15         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57         6.58        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-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
       15.72         6.71         3.58        13.28         4.70         3.29 
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-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-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        30.87        12.89        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-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         3.22         7.36        28.73        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.20         0.99         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
        7.23         0.85        11.61        84.72        10.13        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       14.70        11.84        14.50        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       11.05         5.79        18.05         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        8.98        60.03         2.99       185.16        71.01        11.84 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
        3.42         5.36         1.08        19.96         1.94         6.18 
TCGA-Z2-A8RT TCGA-Z2-AA3V 
        8.22         5.98 

  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                        110.79                         185.16 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                         13.68                          15.22 
[1] "0.1 - 110.8 (13.7)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.2"
D27V2, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3Q13.31) MUTATED    26  30
  DEL PEAK  5(3Q13.31) WILD-TYPE 147 136
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            56                            283 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            30                            136 
$`DEL PEAK  5(3Q13.31) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GP 
      112.57       133.25       113.52       178.32       125.19       137.79 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1I2 TCGA-DA-A1I5 
      129.63        18.12         9.90        25.18       176.55       107.34 
TCGA-DA-A1I7 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A20I 
       61.18        10.16        27.22        94.98       151.27        13.55 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2GC TCGA-EE-A2GH 
       72.07        64.64        56.42        17.92        67.43       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JI 
       89.33        90.97       162.48        51.62       172.18       148.08 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A3EV 
       35.44        13.94        50.76       152.35        37.25        46.98 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A4F8 
        7.00        34.82        48.59        47.38       101.26       174.84 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       77.88        47.54       139.89       117.93        64.44        62.79 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZX TCGA-WE-AAA4 
       12.62        21.37        42.08        38.56        22.68        15.16 
TCGA-YG-AA3P TCGA-Z2-AA3S 
       14.43        93.07 

$`DEL PEAK  5(3Q13.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87        62.07        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      135.75       137.92        18.18        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      161.00        29.06       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
        6.41        11.34        22.29        11.11        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       48.89        36.03       117.21        20.38       194.83        35.93 
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-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        17.85        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       17.29        52.01         6.35        12.20        29.82         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56       168.26        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       63.78         2.60        56.84        18.61        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92       369.93        25.87       195.02        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        59.28       314.56       161.03 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
       48.72        54.74        79.66        75.48       126.81        13.91 
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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
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       158.63       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       134.40        71.21 
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-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       53.19       201.80        27.35        51.35       109.58        31.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        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-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18        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-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
      210.08        15.16        38.27        29.46        94.39       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-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        23.93        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-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        12.43        26.73        49.45 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
        2.04        11.74        84.72        10.13        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       46.36        50.10        59.41        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        6.67        18.05         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 
      121.08         4.01       219.16       105.04        24.03        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.61        90.28        56.98        59.41        52.34         3.75 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT 
       43.73         2.20        30.18        10.36        36.03        23.64 
TCGA-Z2-AA3V 
       11.74 

  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                          7.00                           0.16 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                        208.04                         369.93 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                        63.615                         48.890 
[1] "7.0 - 208.0 (63.6)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1"  
D27V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  5(3Q13.31) MUTATED                    9             2
  DEL PEAK  5(3Q13.31) WILD-TYPE                 52             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  5(3Q13.31) MUTATED                                          14
  DEL PEAK  5(3Q13.31) WILD-TYPE                                        58
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK  5(3Q13.31) MUTATED                    31
  DEL PEAK  5(3Q13.31) WILD-TYPE                 178
D27V4, multiclass
                                           clus
vv                                          DEL PEAK  5(3Q13.31) MUTATED
  DISTANT METASTASIS                                                   9
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           14
  REGIONAL LYMPH NODE                                                 31
                                           clus
vv                                          DEL PEAK  5(3Q13.31) WILD-TYPE
  DISTANT METASTASIS                                                    52
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             58
  REGIONAL LYMPH NODE                                                  178
[1] 4 2
[1] 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(3Q13.31) MUTATED             2       2       5        3        4
  DEL PEAK  5(3Q13.31) WILD-TYPE          10       5      23       14       23
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  5(3Q13.31) MUTATED          2         1         4         2
  DEL PEAK  5(3Q13.31) WILD-TYPE       20        13        15        10
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  5(3Q13.31) MUTATED           6          4          5          7
  DEL PEAK  5(3Q13.31) WILD-TYPE        29         11         27         51
                                vv
clus                             STAGE IV
  DEL PEAK  5(3Q13.31) MUTATED          2
  DEL PEAK  5(3Q13.31) WILD-TYPE       17
D27V5, multiclass
             clus
vv            DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  I OR II NOS                            2                             10
  STAGE 0                                2                              5
  STAGE I                                5                             23
  STAGE IA                               3                             14
  STAGE IB                               4                             23
  STAGE II                               2                             20
  STAGE IIA                              1                             13
  STAGE IIB                              4                             15
  STAGE IIC                              2                             10
  STAGE III                              6                             29
  STAGE IIIA                             4                             11
  STAGE IIIB                             5                             27
  STAGE IIIC                             7                             51
  STAGE IV                               2                             17
[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(3Q13.31) MUTATED      10 12  9 12
  DEL PEAK  5(3Q13.31) WILD-TYPE    53 59 65 55
D27V6, multiclass
       clus
vv      DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  T0+T1                           10                             53
  T2                              12                             59
  T3                               9                             65
  T4                              12                             55
[1] 4 2
[1] 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(3Q13.31) MUTATED    30   7   8   6
  DEL PEAK  5(3Q13.31) WILD-TYPE 138  54  30  41
D27V7, multiclass
    clus
vv   DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  N0                           30                            138
  N1                            7                             54
  N2                            8                             30
  N3                            6                             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                              M0  M1 M1A M1B M1C
  DEL PEAK  5(3Q13.31) MUTATED    50   0   0   0   2
  DEL PEAK  5(3Q13.31) WILD-TYPE 256   4   3   4   7
D27V8, multiclass
     clus
vv    DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  M0                            50                            256
  M1                             0                              4
  M1A                            0                              3
  M1B                            0                              4
  M1C                            2                              7
[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  5(3Q13.31) MUTATED    21  14
  DEL PEAK  5(3Q13.31) WILD-TYPE 108  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     21   14
  DEL PEAK  5(3Q13.31) WILD-TYPE  108   73
     clus
vv    DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  NO                            21                            108
  YES                           14                             73
[1] 2 2
[1] FALSE
D27V10, binary
                                cls
clus                               0   1
  DEL PEAK  5(3Q13.31) MUTATED     4  53
  DEL PEAK  5(3Q13.31) WILD-TYPE  39 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED      4   53
  DEL PEAK  5(3Q13.31) WILD-TYPE   39  251
     clus
vv    DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  NO                             4                             39
  YES                           53                            251
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, binary
                                cls
clus                               0   1
  DEL PEAK  5(3Q13.31) MUTATED    21  36
  DEL PEAK  5(3Q13.31) WILD-TYPE 110 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     21   36
  DEL PEAK  5(3Q13.31) WILD-TYPE  110  181
        clus
vv       DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  FEMALE                           21                            110
  MALE                             36                            181
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3Q13.31) MUTATED       2                         0    52
  DEL PEAK  5(3Q13.31) WILD-TYPE     3                         1   274
D27V13, multiclass
                           clus
vv                          DEL PEAK  5(3Q13.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               52
                           clus
vv                          DEL PEAK  5(3Q13.31) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                274
[1] 3 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  5(3Q13.31) MUTATED     2  54
  DEL PEAK  5(3Q13.31) WILD-TYPE   5 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED      2   54
  DEL PEAK  5(3Q13.31) WILD-TYPE    5  280
                        clus
vv                       DEL PEAK  5(3Q13.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       DEL PEAK  5(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            280
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  6(4P16.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4P16.3) MUTATED    41  40
  DEL PEAK  6(4P16.3) WILD-TYPE 127 125
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           81                           252 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           40                           125 
$`DEL PEAK  6(4P16.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN 
       16.47       111.09        45.83        10.29        88.50        56.19 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       64.44        61.38         9.34       103.59        26.37        29.23 
TCGA-D3-A51F TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GM 
       54.74        47.87        29.72        22.06         4.18        75.65 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH 
        5.72        13.22        35.80        14.83         0.20         0.13 
TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        8.12        60.23         4.34        15.85         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A2A5 
       11.15        36.85         1.08        39.62        32.15         9.67 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM 
       47.21        28.31        55.69         8.84        98.27        56.02 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE 
       21.60        53.16       122.73        15.95        16.14        18.41 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T 
       31.40        12.95         3.52        11.90        36.07         6.58 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A7U8 TCGA-FS-A1Z0 
        1.87        13.08        12.62        11.74         3.58        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZR TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB 
       15.52         7.30         8.81         7.36        14.20         5.98 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
        0.13         0.85        11.61        44.28        10.13        15.42 
TCGA-GN-A8LL TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZX 
       14.50         8.98        10.98        11.84         7.10        21.83 
TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-A8RT 
        1.08         6.18         8.22 

$`DEL PEAK  6(4P16.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         6.97         8.52        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      110.79        28.08        22.55        81.24        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        68.22        86.76        11.41        44.19         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       36.16         6.31        92.42        59.57       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32        82.29        13.32        24.00         6.31 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       93.21        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       25.78       110.24        52.01        13.68        17.72        23.11 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       10.22        15.19       142.45       108.79        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        14.60        48.79        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-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
       13.15        23.15        19.00        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       11.57        10.55         6.31         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29E 
        5.13         4.31         9.21         1.18         7.99        62.79 
TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        8.55         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       30.44         2.43         8.09        11.31        49.22        36.30 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       36.33        51.12        34.29        17.98        60.00        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       19.43        16.01        35.54        33.83         5.42         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
       63.42       125.65       111.91        25.08        26.99        60.49 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67         5.56       124.31        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       22.22         0.95        27.35        21.73        33.60        18.61 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F 
       38.40         5.72        76.41        25.18         3.78        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-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       85.74        15.72         6.71         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
        4.70         3.29        64.47         3.45        11.01        14.24 
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-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65        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-A4FC 
        5.23        53.85         3.22        28.73        10.78         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.99         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        7.23        31.33        84.72        16.24        12.16        14.70 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       11.84        10.65        14.50        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       11.05         5.79        18.05         0.33         0.69       164.19 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       60.03         2.99       185.16        71.01         5.49         6.48 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       18.67        21.07        13.12         3.72         3.42         5.36 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       19.96         1.94        12.07         4.70         6.67         5.98 

  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                         0.13                          0.16 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       122.73                        185.16 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                        14.83                         14.65 
[1] "0.1 - 122.7 (14.8)" "0.2 - 185.2 (14.6)"
[1] "hr=" "1"  
D28V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4P16.3) MUTATED    44  40
  DEL PEAK  6(4P16.3) WILD-TYPE 129 126
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           84                           255 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           40                           126 
$`DEL PEAK  6(4P16.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN 
       16.57       112.04        90.90        43.43       115.53        56.19 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       66.08        86.93         9.34       103.59        39.75        45.30 
TCGA-D3-A51F TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GM 
       55.73       137.92        30.84        79.59        58.52        95.24 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HW 
      151.53        54.67        18.12        11.11        66.25        36.03 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C 
       15.68        10.16        17.85        94.98       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
       91.56        80.61        47.84        13.97        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO 
       56.84       195.02        39.29       208.04        75.48       126.81 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AB 
       21.67       129.27       167.90        43.23       162.48       122.73 
TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19D 
       23.47        34.32        51.35        31.40        13.94        12.59 
TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG 
       13.02        37.25         8.88        23.34        16.37        31.27 
TCGA-ER-A2NH TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZR 
       32.05        15.16       202.65        28.08        27.72        11.41 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 
       66.67       174.84        26.73        47.54         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A8LL TCGA-W3-A825 TCGA-W3-AA1V 
      139.89        10.13        62.79        21.37        63.02        42.08 
TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-A8RT 
       24.03         8.61        22.68         2.20        36.03        23.64 

$`DEL PEAK  6(4P16.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.67       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        31.59        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       168.00        86.76        11.87        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32       166.52        60.23        24.53        13.87 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
      174.84        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       125.79       135.75       178.32        18.18       125.19 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       11.61        15.19       228.99       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1JX 
      137.79        29.06       129.63       117.17         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       11.34        22.29         9.90        25.18        22.95        48.89 
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-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       10.49       215.44        13.87        68.25        54.02        17.29 
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-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20H 
       33.73        14.70        26.89        68.15         4.96       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P 
       13.55        63.35        63.78        72.07        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
       37.35        14.47        55.92       369.93        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03        48.72        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
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       158.63       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65       134.40        71.21        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        54.51        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        53.19       201.80        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      109.58       148.08        35.44        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        48.89        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-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       79.99        43.82        20.15       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       210.08 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        7.00        38.27        34.82        29.46        94.39       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       48.59       228.59        20.91         7.79        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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26        74.73       133.55       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73        12.43        49.45        77.88         0.20        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
        0.16        19.30         9.90         7.23       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       64.44        32.48        39.58        46.36        12.62        50.10 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.33         0.69       212.22       121.08         4.01       219.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        38.56        54.38        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       52.34         3.75        43.73        30.18        10.36        15.16 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        93.07        11.74 

  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                         2.04                          0.16 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       208.04                        369.93 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       42.655                        52.340 
[1] "2.0 - 208.0 (42.7)" "0.2 - 369.9 (52.3)"
[1] "hr=" "1.2"
D28V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  6(4P16.3) MUTATED                   13             3
  DEL PEAK  6(4P16.3) WILD-TYPE                 48             2
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  6(4P16.3) MUTATED                                          21
  DEL PEAK  6(4P16.3) WILD-TYPE                                        51
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  6(4P16.3) MUTATED                    48
  DEL PEAK  6(4P16.3) WILD-TYPE                 161
D28V4, multiclass
                                           clus
vv                                          DEL PEAK  6(4P16.3) MUTATED
  DISTANT METASTASIS                                                 13
  PRIMARY TUMOR                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          21
  REGIONAL LYMPH NODE                                                48
                                           clus
vv                                          DEL PEAK  6(4P16.3) WILD-TYPE
  DISTANT METASTASIS                                                   48
  PRIMARY TUMOR                                                         2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            51
  REGIONAL LYMPH NODE                                                 161
[1] 4 2
[1] 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(4P16.3) MUTATED             1       2       7        3        6
  DEL PEAK  6(4P16.3) WILD-TYPE          11       5      21       14       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  6(4P16.3) MUTATED          7         1         7         3
  DEL PEAK  6(4P16.3) WILD-TYPE       15        13        12         9
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  6(4P16.3) MUTATED           8          5         12         14
  DEL PEAK  6(4P16.3) WILD-TYPE        27         10         20         44
                               vv
clus                            STAGE IV
  DEL PEAK  6(4P16.3) MUTATED          2
  DEL PEAK  6(4P16.3) WILD-TYPE       17
D28V5, multiclass
             clus
vv            DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  I OR II NOS                           1                            11
  STAGE 0                               2                             5
  STAGE I                               7                            21
  STAGE IA                              3                            14
  STAGE IB                              6                            21
  STAGE II                              7                            15
  STAGE IIA                             1                            13
  STAGE IIB                             7                            12
  STAGE IIC                             3                             9
  STAGE III                             8                            27
  STAGE IIIA                            5                            10
  STAGE IIIB                           12                            20
  STAGE IIIC                           14                            44
  STAGE IV                              2                            17
[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(4P16.3) MUTATED      15 18 19 16
  DEL PEAK  6(4P16.3) WILD-TYPE    48 53 55 51
D28V6, multiclass
       clus
vv      DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  T0+T1                          15                            48
  T2                             18                            53
  T3                             19                            55
  T4                             16                            51
[1] 4 2
[1] 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(4P16.3) MUTATED    36  19  10  12
  DEL PEAK  6(4P16.3) WILD-TYPE 132  42  28  35
D28V7, multiclass
    clus
vv   DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  N0                          36                           132
  N1                          19                            42
  N2                          10                            28
  N3                          12                            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                             M0  M1 M1A M1B M1C
  DEL PEAK  6(4P16.3) MUTATED    76   0   1   1   1
  DEL PEAK  6(4P16.3) WILD-TYPE 230   4   2   3   8
D28V8, multiclass
     clus
vv    DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  M0                           76                           230
  M1                            0                             4
  M1A                           1                             2
  M1B                           1                             3
  M1C                           1                             8
[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  6(4P16.3) MUTATED   33 22
  DEL PEAK  6(4P16.3) WILD-TYPE 96 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     33   22
  DEL PEAK  6(4P16.3) WILD-TYPE   96   65
     clus
vv    DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  NO                           33                            96
  YES                          22                            65
[1] 2 2
[1] FALSE
D28V10, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    10  76
  DEL PEAK  6(4P16.3) WILD-TYPE  33 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     10   76
  DEL PEAK  6(4P16.3) WILD-TYPE   33  228
     clus
vv    DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  NO                           10                            33
  YES                          76                           228
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    33  53
  DEL PEAK  6(4P16.3) WILD-TYPE  98 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     33   53
  DEL PEAK  6(4P16.3) WILD-TYPE   98  164
        clus
vv       DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          33                            98
  MALE                            53                           164
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4P16.3) MUTATED       2                         0    80
  DEL PEAK  6(4P16.3) WILD-TYPE     3                         1   246
D28V13, multiclass
                           clus
vv                          DEL PEAK  6(4P16.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              80
                           clus
vv                          DEL PEAK  6(4P16.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               246
[1] 3 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  6(4P16.3) MUTATED     1  83
  DEL PEAK  6(4P16.3) WILD-TYPE   6 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED      1   83
  DEL PEAK  6(4P16.3) WILD-TYPE    6  251
                        clus
vv                       DEL PEAK  6(4P16.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          83
                        clus
vv                       DEL PEAK  6(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           251
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  7(4Q34.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q34.3) MUTATED    54  46
  DEL PEAK  7(4Q34.3) WILD-TYPE 114 119
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          100                           233 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           46                           119 
$`DEL PEAK  7(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        29.23        54.74 
TCGA-D3-A51N TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
       21.44        22.06        75.65       124.47        87.62         5.56 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I7 
        5.72         9.90        13.22        35.80        51.12        36.69 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 
       17.56        14.83         0.20        13.35        10.55         8.12 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T 
        1.12        60.23         9.21        37.97        39.62        30.44 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GI 
       32.15         8.09         9.67        36.33        47.21        30.08 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM 
       28.31        55.69        36.33         8.84        98.27        56.02 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA 
       21.60        52.67        15.95        22.92        16.14        22.22 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B 
        0.95        27.35        18.41        31.40        12.95        25.18 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
        3.52        11.90        36.07         1.87        12.62        11.74 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        6.58        22.49         3.58         5.36        23.80        15.52 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        7.30        20.38        19.53        11.08         7.17        12.92 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A4U9 
        0.20         0.13         0.85        11.61        10.13        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-A828 
       14.50        14.50        15.81        18.05         8.98        60.03 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-AA9Y 
       10.98        11.84         7.10        18.67        21.83         1.08 
TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
        1.94         6.18         8.22         6.67 

$`DEL PEAK  7(4Q34.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         6.97         8.52        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
        8.38        21.14        68.22        86.76        44.19         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       36.16         6.31        92.42        59.57       114.67        15.25 
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-A3MU TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       26.37        93.21        31.30        54.31        32.28        32.61 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       25.78       110.24        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       23.11        29.72        10.22        15.19         4.18       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      108.79        38.93        11.44        24.07         4.01        21.93 
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        23.15        19.00 
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        15.85         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        62.79         8.55        36.85         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        36.30        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       60.00        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
       63.42       125.65       111.91        25.08        26.99        60.49 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16         5.56       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
       30.15        13.81        12.72         3.22        21.60        21.60 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       21.73        33.60        18.61        38.40         5.72        76.41 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.78        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       28.60        42.84        34.68         9.57         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL 
       78.44        11.80         1.51        13.08         9.04         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7UA 
        5.62        18.41        85.74        15.72         6.71        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        2.20         4.70         3.29        64.47         3.45        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZK 
       14.24         7.33         3.39         8.22        30.87        12.89 
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-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-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.99         0.16        17.33         9.90         7.23 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        14.50         0.43        11.05         5.79 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 
        0.33         0.69       164.19         2.99       185.16        71.01 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        5.49         6.48        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3V 
        5.36        19.96        12.07         4.70         5.98 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                         0.13                          0.13 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       124.47                        185.16 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       16.305                        14.200 
[1] "0.1 - 124.5 (16.3)" "0.1 - 185.2 (14.2)"
[1] "hr=" "1.1"
D29V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q34.3) MUTATED    56  46
  DEL PEAK  7(4Q34.3) WILD-TYPE 117 120
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                          102                           237 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           46                           120 
$`DEL PEAK  7(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        45.30        55.73 
TCGA-D3-A51N TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
       22.62        79.59        95.24       161.00       137.79       129.63 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW 
      151.53        54.67        11.11         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        17.29 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29C 
       27.22        94.98        33.73       133.81       168.26        47.84 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 
       56.84       369.93       195.02        17.92        39.29        86.14 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GU TCGA-EE-A2M5 
      208.04        48.72        75.48       126.81        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        71.21        23.47       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 
       34.32        53.19       201.80        27.35        51.35        31.40 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A2ND 
       13.94        98.40        12.59        13.02        37.25        23.34 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FR-A7U9 
       31.27        32.05        80.32        46.98        15.16         7.00 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
      202.65        28.08        27.72       357.37        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 
        9.70        47.38         0.20        47.54         2.04        11.74 
TCGA-GN-A266 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-QB-AA9O 
       10.13        12.62        50.10        21.37        65.88        18.05 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM 
       63.02       121.08        42.08        24.03         8.61        90.28 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       22.68         2.20        10.36        36.03        23.64        93.07 

$`DEL PEAK  7(4Q34.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.67       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       65.49        23.77       168.00        86.76        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        59.57       130.72        58.06 
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-A3MU TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       39.75       174.84        56.35       145.12        32.94        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
      125.19        30.84        11.61        15.19        58.52       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1JX 
      170.20        89.13        29.06       117.17         3.65         6.41 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       18.12        11.34        22.29        25.18        22.95        48.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       20.38       194.83       176.55        35.93       107.34        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q 
       65.92        23.44        68.09        28.60        10.49        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       17.85        68.25        54.02        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       29.82         8.65        14.70        26.89        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
      151.27        91.56        13.55        63.35        80.61        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       63.78        72.07        64.64         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
       37.35        14.47        55.92        25.87        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
       36.82        59.28        67.43       314.56       161.03        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
      203.05        47.54       248.65       134.40       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-EE-A3JI 
      138.81       172.18        36.95        64.08       109.58       148.08 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19F 
       35.44        50.76         9.17        77.75        48.89        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       20.15        16.37       247.04        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      174.21        15.72       210.08        38.27        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       94.39       216.92        48.59       228.59        20.91         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       48.85        53.52        32.75        23.93       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-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-FS-A4FD TCGA-FW-A3R5 
      174.84        12.43        26.73        49.45        77.88        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 
        0.16        19.30         9.90         7.23       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       84.72        64.44        62.79        32.48        39.58        46.36 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       59.41       357.04       294.77         6.67         0.33         0.69 
TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
      212.22         4.01       219.16       105.04        38.56        54.38 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 
       56.98        59.41        52.34         3.75        43.73        30.18 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3V 
       15.16        14.43        11.74 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                         0.20                          0.16 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       369.93                        357.04 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        46.98                         53.16 
[1] "0.2 - 369.9 (47.0)" "0.2 - 357.0 (53.2)"
[1] "hr=" "1"  
D29V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  7(4Q34.3) MUTATED                   21             2
  DEL PEAK  7(4Q34.3) WILD-TYPE                 40             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  7(4Q34.3) MUTATED                                          23
  DEL PEAK  7(4Q34.3) WILD-TYPE                                        49
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  7(4Q34.3) MUTATED                    56
  DEL PEAK  7(4Q34.3) WILD-TYPE                 153
D29V4, multiclass
                                           clus
vv                                          DEL PEAK  7(4Q34.3) MUTATED
  DISTANT METASTASIS                                                 21
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          23
  REGIONAL LYMPH NODE                                                56
                                           clus
vv                                          DEL PEAK  7(4Q34.3) WILD-TYPE
  DISTANT METASTASIS                                                   40
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            49
  REGIONAL LYMPH NODE                                                 153
[1] 4 2
[1] 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(4Q34.3) MUTATED             2       2       7        5        9
  DEL PEAK  7(4Q34.3) WILD-TYPE          10       5      21       12       18
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  7(4Q34.3) MUTATED          7         0         4         5
  DEL PEAK  7(4Q34.3) WILD-TYPE       15        14        15         7
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  7(4Q34.3) MUTATED          10          6         15         19
  DEL PEAK  7(4Q34.3) WILD-TYPE        25          9         17         39
                               vv
clus                            STAGE IV
  DEL PEAK  7(4Q34.3) MUTATED          4
  DEL PEAK  7(4Q34.3) WILD-TYPE       15
D29V5, multiclass
             clus
vv            DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  I OR II NOS                           2                            10
  STAGE 0                               2                             5
  STAGE I                               7                            21
  STAGE IA                              5                            12
  STAGE IB                              9                            18
  STAGE II                              7                            15
  STAGE IIA                             0                            14
  STAGE IIB                             4                            15
  STAGE IIC                             5                             7
  STAGE III                            10                            25
  STAGE IIIA                            6                             9
  STAGE IIIB                           15                            17
  STAGE IIIC                           19                            39
  STAGE IV                              4                            15
[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(4Q34.3) MUTATED      19 21 22 17
  DEL PEAK  7(4Q34.3) WILD-TYPE    44 50 52 50
D29V6, multiclass
       clus
vv      DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  T0+T1                          19                            44
  T2                             21                            50
  T3                             22                            52
  T4                             17                            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
  DEL PEAK  7(4Q34.3) MUTATED    42  23  12  16
  DEL PEAK  7(4Q34.3) WILD-TYPE 126  38  26  31
D29V7, multiclass
    clus
vv   DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  N0                          42                           126
  N1                          23                            38
  N2                          12                            26
  N3                          16                            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  7(4Q34.3) MUTATED    92   1   0   2   2
  DEL PEAK  7(4Q34.3) WILD-TYPE 214   3   3   2   7
D29V8, multiclass
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  M0                           92                           214
  M1                            1                             3
  M1A                           0                             3
  M1B                           2                             2
  M1C                           2                             7
[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  7(4Q34.3) MUTATED   35 26
  DEL PEAK  7(4Q34.3) WILD-TYPE 94 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     35   26
  DEL PEAK  7(4Q34.3) WILD-TYPE   94   61
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                           35                            94
  YES                          26                            61
[1] 2 2
[1] FALSE
D29V10, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED    17  86
  DEL PEAK  7(4Q34.3) WILD-TYPE  26 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     17   86
  DEL PEAK  7(4Q34.3) WILD-TYPE   26  218
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                           17                            26
  YES                          86                           218
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED    46  57
  DEL PEAK  7(4Q34.3) WILD-TYPE  85 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED     46   57
  DEL PEAK  7(4Q34.3) WILD-TYPE   85  160
        clus
vv       DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  FEMALE                          46                            85
  MALE                            57                           160
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q34.3) MUTATED       2                         0    94
  DEL PEAK  7(4Q34.3) WILD-TYPE     3                         1   232
D29V13, multiclass
                           clus
vv                          DEL PEAK  7(4Q34.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              94
                           clus
vv                          DEL PEAK  7(4Q34.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               232
[1] 3 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  7(4Q34.3) MUTATED     1  99
  DEL PEAK  7(4Q34.3) WILD-TYPE   6 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      1   99
  DEL PEAK  7(4Q34.3) WILD-TYPE    6  235
                        clus
vv                       DEL PEAK  7(4Q34.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       DEL PEAK  7(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           235
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  8(5P15.31) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(5P15.31) MUTATED    34  37
  DEL PEAK  8(5P15.31) WILD-TYPE 134 128
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            71                            262 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            37                            128 
$`DEL PEAK  8(5P15.31) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
        6.97         8.52        68.22        11.41         7.50        92.42 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GN 
       61.38        24.00        29.23        47.87        29.72       124.47 
TCGA-D3-A8GR TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-EB-A44Q 
        5.56         5.72        48.79        35.80        17.56        13.15 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 TCGA-EE-A185 
        0.20        13.35        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        36.30        51.12 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2MM 
       17.98        60.00        47.21        30.08         1.15        56.02 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
       21.60         5.56        21.60        21.60        22.22         0.95 
TCGA-ER-A199 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A69P TCGA-FS-A1ZD 
        5.72         1.87         1.51        12.62        15.72         8.22 
TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F8 
       47.38        40.64        27.39         0.82         3.22        14.20 
TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        5.98         0.20         0.85        44.28        31.33        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH 
       16.24        15.42        14.70        14.50        14.50        15.81 
TCGA-OD-A75X TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       11.05        18.67        21.83         5.36        12.07 

$`DEL PEAK  8(5P15.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97        16.47       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.79        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       85.32         8.38        21.14        88.50        86.76        44.19 
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        59.57       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML 
       15.25        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        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       52.01        13.68        17.72        23.11        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       87.62        11.44        24.07         4.01        21.93         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        13.22        14.60        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-A3F3 TCGA-DA-A3F8 TCGA-EB-A5KH 
       22.36         6.64        19.36         7.00        14.83         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 
       23.15        19.00        13.22         0.20         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
        1.12         1.35        12.20        60.23         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        9.21         7.99         9.90        11.15        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       36.85         1.08        39.62         9.50         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       30.44         2.43        32.15         8.09        11.31        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
        9.67        36.33        34.29        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83        55.69         5.42        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
       63.42       125.65       111.91        25.08        26.99        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16        52.67       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        27.35        18.41        21.73        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       18.61        12.95        38.40        76.41        25.18         3.78 
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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NH 
        6.58        17.72        78.44        11.80        13.08        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       85.74         6.71         3.58         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.70         3.29        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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ 
       52.08         8.65         8.81        49.15         8.68         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       53.85         7.36        28.73        10.78         6.41         2.27 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A9SD 
       11.61        84.72        12.16        11.84        10.65        14.50 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.43         5.79        18.05         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        8.98        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       11.84         5.49         6.48         7.10        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
        3.72         3.42         1.08        19.96         1.94         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                          0.20                           0.13 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                        124.47                         185.16 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                         14.50                          15.01 
[1] "0.2 - 124.5 (14.5)" "0.1 - 185.2 (15.0)"
[1] "hr=" "1.2"
D30V2, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(5P15.31) MUTATED    35  37
  DEL PEAK  8(5P15.31) WILD-TYPE 138 129
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            72                            267 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                            37                            129 
$`DEL PEAK  8(5P15.31) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       12.99        16.67       168.00        11.87       113.52       171.58 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GN 
       86.93        24.53        45.30       137.92        30.84       161.00 
TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 
      129.63        18.12        11.11        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        17.29        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        36.82 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GR 
       59.28       314.56       161.03       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-EE-A3JB TCGA-ER-A199 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-FR-A69P 
      201.80         9.17        23.34        20.15        31.27        15.72 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 
       53.52       101.26        53.16        49.48        27.09        50.14 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
      174.84        26.73         0.20         2.04       139.89       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A8LL 
       10.13        64.44        62.79        39.58        50.10        21.37 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       65.88       294.77        90.28        22.68        43.73        15.16 

$`DEL PEAK  8(5P15.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
      103.10        65.49        23.77       115.53        86.76        62.07 
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        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML 
       58.06        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       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      135.75       178.32        18.18       125.19        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      137.79        29.06       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34        22.29         9.90        25.18        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-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-A3F8 TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       28.60        10.49        15.68        17.85        68.25        54.02 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       52.01         6.35        12.20         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       14.70        26.89       133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        2.60        56.84        18.61        14.47        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
       25.87       195.02        17.92        46.82       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       86.14        67.43        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97       126.81        13.91        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      158.63       203.05        47.54       248.65       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       13.81        23.47       138.81       172.18       127.20        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94        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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
      148.18        79.99        43.82        16.37        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      210.08        15.16         7.00        38.27        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       94.39       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-A1ZE 
       28.08         7.79        27.72        48.85       357.37        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       15.45         9.70        32.75        47.38        23.93        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
      133.55        11.41       148.80        26.56        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       66.67        28.73        12.43        49.45        77.88        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 
       47.54         0.16        19.30         9.90         7.23        11.74 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-LH-A9QB 
       84.72        32.48        46.36        12.62        59.41       357.04 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        6.67        18.05         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      121.08         4.01        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       38.56        54.38         8.61        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
        3.75         2.20        30.18        10.36        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                          0.20                           0.16 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                        314.56                         369.93 
  DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE 
                         46.57                          52.34 
[1] "0.2 - 314.6 (46.6)" "0.2 - 369.9 (52.3)"
[1] "hr=" "1.1"
D30V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  8(5P15.31) MUTATED                   15             0
  DEL PEAK  8(5P15.31) WILD-TYPE                 46             5
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  8(5P15.31) MUTATED                                          19
  DEL PEAK  8(5P15.31) WILD-TYPE                                        53
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK  8(5P15.31) MUTATED                    41
  DEL PEAK  8(5P15.31) WILD-TYPE                 168
D30V4, multiclass
                                           clus
vv                                          DEL PEAK  8(5P15.31) MUTATED
  DISTANT METASTASIS                                                  15
  PRIMARY TUMOR                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           19
  REGIONAL LYMPH NODE                                                 41
                                           clus
vv                                          DEL PEAK  8(5P15.31) WILD-TYPE
  DISTANT METASTASIS                                                    46
  PRIMARY TUMOR                                                          5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             53
  REGIONAL LYMPH NODE                                                  168
[1] 4 2
[1] 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(5P15.31) MUTATED             3       3       5        3        4
  DEL PEAK  8(5P15.31) WILD-TYPE           9       4      23       14       23
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  8(5P15.31) MUTATED          2         2         5         6
  DEL PEAK  8(5P15.31) WILD-TYPE       20        12        14         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  8(5P15.31) MUTATED           6          4         11         12
  DEL PEAK  8(5P15.31) WILD-TYPE        29         11         21         46
                                vv
clus                             STAGE IV
  DEL PEAK  8(5P15.31) MUTATED          2
  DEL PEAK  8(5P15.31) WILD-TYPE       17
D30V5, multiclass
             clus
vv            DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  I OR II NOS                            3                              9
  STAGE 0                                3                              4
  STAGE I                                5                             23
  STAGE IA                               3                             14
  STAGE IB                               4                             23
  STAGE II                               2                             20
  STAGE IIA                              2                             12
  STAGE IIB                              5                             14
  STAGE IIC                              6                              6
  STAGE III                              6                             29
  STAGE IIIA                             4                             11
  STAGE IIIB                            11                             21
  STAGE IIIC                            12                             46
  STAGE IV                               2                             17
[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(5P15.31) MUTATED       9 16 12 19
  DEL PEAK  8(5P15.31) WILD-TYPE    54 55 62 48
D30V6, multiclass
       clus
vv      DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  T0+T1                            9                             54
  T2                              16                             55
  T3                              12                             62
  T4                              19                             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  8(5P15.31) MUTATED    31  18   7   9
  DEL PEAK  8(5P15.31) WILD-TYPE 137  43  31  38
D30V7, multiclass
    clus
vv   DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  N0                           31                            137
  N1                           18                             43
  N2                            7                             31
  N3                            9                             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                              M0  M1 M1A M1B M1C
  DEL PEAK  8(5P15.31) MUTATED    64   1   0   0   1
  DEL PEAK  8(5P15.31) WILD-TYPE 242   3   3   4   8
D30V8, multiclass
     clus
vv    DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  M0                            64                            242
  M1                             1                              3
  M1A                            0                              3
  M1B                            0                              4
  M1C                            1                              8
[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  8(5P15.31) MUTATED    20  26
  DEL PEAK  8(5P15.31) WILD-TYPE 109  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED     20   26
  DEL PEAK  8(5P15.31) WILD-TYPE  109   61
     clus
vv    DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  NO                            20                            109
  YES                           26                             61
[1] 2 2
[1] FALSE
D30V10, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.31) MUTATED     6  69
  DEL PEAK  8(5P15.31) WILD-TYPE  37 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED      6   69
  DEL PEAK  8(5P15.31) WILD-TYPE   37  235
     clus
vv    DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  NO                             6                             37
  YES                           69                            235
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, binary
                                cls
clus                               0   1
  DEL PEAK  8(5P15.31) MUTATED    35  40
  DEL PEAK  8(5P15.31) WILD-TYPE  96 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED     35   40
  DEL PEAK  8(5P15.31) WILD-TYPE   96  177
        clus
vv       DEL PEAK  8(5P15.31) MUTATED DEL PEAK  8(5P15.31) WILD-TYPE
  FEMALE                           35                             96
  MALE                             40                            177
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5P15.31) MUTATED       3                         1    65
  DEL PEAK  8(5P15.31) WILD-TYPE     2                         0   261
D30V13, multiclass
                           clus
vv                          DEL PEAK  8(5P15.31) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               65
                           clus
vv                          DEL PEAK  8(5P15.31) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                261
[1] 3 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  8(5P15.31) MUTATED     0  71
  DEL PEAK  8(5P15.31) WILD-TYPE   7 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(5P15.31) MUTATED      0   71
  DEL PEAK  8(5P15.31) WILD-TYPE    7  263
                        clus
vv                       DEL PEAK  8(5P15.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       DEL PEAK  8(5P15.31) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            263
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(5Q12.1) MUTATED    42  44
  DEL PEAK  9(5Q12.1) WILD-TYPE 126 121
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           86                           247 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           44                           121 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JL 
        6.97        28.08        22.55        11.41         6.31        92.42 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GL TCGA-D3-A5GN 
       64.44        15.25        61.38        29.23       110.24        52.01 
TCGA-D3-A5GO TCGA-D3-A8GI TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV 
       47.87         4.18         4.01         5.72        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F5 
       35.80        10.03        44.52        36.69         6.64        17.56 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29C 
       13.35        11.57        10.55         4.31         9.21        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2A2 
       11.15        62.79        39.62        12.03         2.43        36.30 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        47.21        30.08 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AB 
       28.31         1.15        63.42        56.02        26.99       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB 
        3.68        30.15        12.72        21.60        21.60         0.95 
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        15.72         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         0.85 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-HR-A2OH 
       44.28        10.13        16.24        15.42        14.50        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8ZX 
        0.43        11.05        18.05         8.98        10.98        21.83 
TCGA-WE-A8ZY TCGA-WE-AAA4 
        5.36        12.07 

$`DEL PEAK  9(5Q12.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97        16.47         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       70.16       110.79        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        86.76        44.19 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
        7.50        36.16        56.19        59.57       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-A51J 
      103.59        26.37        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
       32.28        21.44        32.61        25.78        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       23.11        29.72        22.06        10.22        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      108.79        38.93        75.65       124.47        87.62        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
        5.56        24.07        21.93         9.90        11.31        14.60 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA 
       51.12        39.19        13.68         9.99        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       22.36        19.36         7.00        14.83        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Z 
        0.13        23.15        19.00        13.22         0.20         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
        8.12         1.12         1.35        12.20         5.13        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
        4.34        15.85         1.18         7.99         9.90         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       36.85         1.08         9.50         8.09         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
       30.44        32.15         8.09        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       36.33        19.43        16.01        35.54        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        5.42        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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
       44.25         7.96        14.56       125.65       111.91        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       51.62        13.81        15.95         3.22        22.92        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35        18.41        21.73        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       18.61        12.95        38.40        76.41         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90        11.11       114.15         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 
       22.49         1.71         5.62        18.41         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        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-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        12.92        47.38        52.08         8.81        49.15 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
        8.68         5.23        53.85         7.36        28.73        10.78 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
       17.33         9.90         7.23        11.61        31.33        84.72 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
        5.79         0.33         0.69       164.19        60.03         2.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      185.16        71.01        11.84         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       18.67        21.07        13.12         3.72         3.42         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.96         1.94         6.18         4.70         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         0.43                          0.13 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       122.73                        185.16 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                        15.57                         14.56 
[1] "0.4 - 122.7 (15.6)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1.1"
D31V2, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(5Q12.1) MUTATED    43  45
  DEL PEAK  9(5Q12.1) WILD-TYPE 130 121
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           88                           251 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           45                           121 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JL 
       12.99        28.08        31.59        11.87        12.10       171.58 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GL TCGA-D3-A5GN 
       66.08        58.06        86.93        45.30       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A8GI TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      137.92        58.52       151.53         6.41        11.34        11.11 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
       66.25        48.89        36.03        20.38       107.34        61.18 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 
       68.09       215.44        17.29        29.82        27.22         4.96 
TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P 
      168.26        47.84        13.97        63.78        56.84        56.42 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       25.87        36.82        59.28        67.43       314.56       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MM 
      208.04        48.72        75.48        14.30        96.23       167.90 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 
      248.65       122.73         3.68        54.51       138.81        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A2ND 
       64.08       201.80         9.17        98.40       152.35        23.34 
TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZK 
       20.15        32.05       174.21        15.72        48.59        23.93 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F8 
      133.55        53.16        49.48        27.09        50.14       174.84 
TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       26.73         2.04       139.89        10.13        64.44        62.79 
TCGA-GN-A8LK TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-W3-A825 
       50.10        65.88       357.04       294.77        18.05        63.02 
TCGA-W3-AA1V TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       42.08        22.68        43.73        15.16 

$`DEL PEAK  9(5Q12.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       71.80       133.25        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        86.76        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
      113.52        42.08        56.19        59.57       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-A51J 
      103.59        39.75       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
       32.94        22.62        63.81        26.89       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      125.19        30.84        79.59        11.61        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      170.20        89.13        95.24       161.00       137.79        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z3 
      129.63       117.17        54.67         3.65        18.12        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        25.18        22.95       117.21       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       35.93        53.92        65.92        23.44        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        68.25        54.02 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       52.01         6.35        12.20         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89        68.15       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       13.55        63.35        80.61        72.07        64.64         2.60 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       18.61        37.35        14.47        55.92       369.93       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GJ 
       17.92        46.82       102.90        39.29        86.14        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       54.74        79.66        90.97       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      204.66       158.63       203.05        47.54        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
      162.48        71.21        53.26       124.31        51.62        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       23.47       172.18       127.20        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       50.76        77.75        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      268.93         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.37        31.27       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
        6.77        92.98       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       34.82        29.46        94.39       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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ 
      101.26        74.73        11.41       148.80        26.56        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       77.82        66.67        28.73        12.43        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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D 
        7.23        11.74       117.93        84.72        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A693 
       46.36        12.62        21.37        59.41         6.67         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 
        0.69       212.22       121.08         4.01       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        38.56        54.38         8.61        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.41        52.34         3.75         2.20        30.18        10.36 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        23.64        93.07        11.74 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         2.04                          0.16 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       357.04                        369.93 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       53.835                        48.890 
[1] "2.0 - 357.0 (53.8)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1"  
D31V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  9(5Q12.1) MUTATED                   18             1
  DEL PEAK  9(5Q12.1) WILD-TYPE                 43             4
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK  9(5Q12.1) MUTATED                                          22
  DEL PEAK  9(5Q12.1) WILD-TYPE                                        50
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  9(5Q12.1) MUTATED                    52
  DEL PEAK  9(5Q12.1) WILD-TYPE                 157
D31V4, multiclass
                                           clus
vv                                          DEL PEAK  9(5Q12.1) MUTATED
  DISTANT METASTASIS                                                 18
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          22
  REGIONAL LYMPH NODE                                                52
                                           clus
vv                                          DEL PEAK  9(5Q12.1) WILD-TYPE
  DISTANT METASTASIS                                                   43
  PRIMARY TUMOR                                                         4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            50
  REGIONAL LYMPH NODE                                                 157
[1] 4 2
[1] 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(5Q12.1) MUTATED             4       2       9        4        5
  DEL PEAK  9(5Q12.1) WILD-TYPE           8       5      19       13       22
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  9(5Q12.1) MUTATED          7         1         5         4
  DEL PEAK  9(5Q12.1) WILD-TYPE       15        13        14         8
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  9(5Q12.1) MUTATED           8          3         12         16
  DEL PEAK  9(5Q12.1) WILD-TYPE        27         12         20         42
                               vv
clus                            STAGE IV
  DEL PEAK  9(5Q12.1) MUTATED          3
  DEL PEAK  9(5Q12.1) WILD-TYPE       16
D31V5, multiclass
             clus
vv            DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  I OR II NOS                           4                             8
  STAGE 0                               2                             5
  STAGE I                               9                            19
  STAGE IA                              4                            13
  STAGE IB                              5                            22
  STAGE II                              7                            15
  STAGE IIA                             1                            13
  STAGE IIB                             5                            14
  STAGE IIC                             4                             8
  STAGE III                             8                            27
  STAGE IIIA                            3                            12
  STAGE IIIB                           12                            20
  STAGE IIIC                           16                            42
  STAGE IV                              3                            16
[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(5Q12.1) MUTATED      16 19 17 20
  DEL PEAK  9(5Q12.1) WILD-TYPE    47 52 57 47
D31V6, multiclass
       clus
vv      DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T0+T1                          16                            47
  T2                             19                            52
  T3                             17                            57
  T4                             20                            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  9(5Q12.1) MUTATED    42  20   8  13
  DEL PEAK  9(5Q12.1) WILD-TYPE 126  41  30  34
D31V7, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  N0                          42                           126
  N1                          20                            41
  N2                           8                            30
  N3                          13                            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  9(5Q12.1) MUTATED    82   0   1   2   1
  DEL PEAK  9(5Q12.1) WILD-TYPE 224   4   2   2   8
D31V8, multiclass
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  M0                           82                           224
  M1                            0                             4
  M1A                           1                             2
  M1B                           2                             2
  M1C                           1                             8
[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  9(5Q12.1) MUTATED   30 24
  DEL PEAK  9(5Q12.1) WILD-TYPE 99 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     30   24
  DEL PEAK  9(5Q12.1) WILD-TYPE   99   63
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                           30                            99
  YES                          24                            63
[1] 2 2
[1] FALSE
D31V10, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED     9  84
  DEL PEAK  9(5Q12.1) WILD-TYPE  34 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      9   84
  DEL PEAK  9(5Q12.1) WILD-TYPE   34  220
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                            9                            34
  YES                          84                           220
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    37  56
  DEL PEAK  9(5Q12.1) WILD-TYPE  94 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     37   56
  DEL PEAK  9(5Q12.1) WILD-TYPE   94  161
        clus
vv       DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  FEMALE                          37                            94
  MALE                            56                           161
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q12.1) MUTATED       1                         0    87
  DEL PEAK  9(5Q12.1) WILD-TYPE     4                         1   239
D31V13, multiclass
                           clus
vv                          DEL PEAK  9(5Q12.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              87
                           clus
vv                          DEL PEAK  9(5Q12.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               239
[1] 3 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  9(5Q12.1) MUTATED     0  89
  DEL PEAK  9(5Q12.1) WILD-TYPE   7 245
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      0   89
  DEL PEAK  9(5Q12.1) WILD-TYPE    7  245
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          89
                        clus
vv                       DEL PEAK  9(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           245
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 10(5Q31.3) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(5Q31.3) MUTATED    53  63
  DEL PEAK 10(5Q31.3) WILD-TYPE 115 102
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                          116                           217 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                           63                           102 
$`DEL PEAK 10(5Q31.3) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JG 
        6.97         8.52        28.08        22.55        11.41         7.50 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
        6.31        92.42        64.44        15.25        61.38        24.00 
TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GI 
       29.23        21.44       110.24        52.01        47.87         4.18 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      142.45        75.65       124.47         4.01         5.72         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-EB-A5UL 
       36.69        25.15        17.56         0.13        19.00        13.35 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A185 TCGA-EE-A20H 
       11.57        10.55         6.31         8.12         4.31         9.21 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P 
        1.18        37.97        62.79         8.55        39.62        12.03 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB 
        9.99         2.43         8.09        11.31        36.30        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MG 
       28.31         1.15        34.98        98.27         2.70        44.25 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AB 
       63.42        56.02        26.99        21.60        60.49       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
        3.68        30.15        12.72        21.60        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19H 
        0.95        33.60        18.61         5.72        25.18        34.88 
TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P 
        9.57         1.87         1.51        11.74        85.74        15.72 
TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        3.45         3.39        20.38        11.08        47.38         8.65 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       40.64        27.39        53.85        28.73        14.20         5.98 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK 
        0.85        44.28        10.13        16.24        15.42        14.50 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-A828 TCGA-WE-A8ZM TCGA-WE-A8ZX 
       15.81        11.05         8.98        60.03        18.67        21.83 
TCGA-WE-A8ZY TCGA-WE-AAA4 
        5.36        12.07 

$`DEL PEAK 10(5Q31.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97        16.47       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      110.79        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH 
       21.14        88.50        68.22        86.76        44.19        36.16 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        59.57       114.67        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        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       54.74        31.30        54.31        32.28        32.61        25.78 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       13.68        17.72        23.11        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       15.19       108.79        38.93        87.62        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 
       24.07        21.93        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        23.15        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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
       15.85         7.99         9.90        11.15        36.85         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        30.44        32.15        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
        9.67        36.33        16.01        35.54        33.83        55.69 
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-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
        9.53        29.46         2.73         7.96        14.56       125.65 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      111.91        25.08        53.16        52.67         5.56       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA 
       51.62        13.81        15.95         3.22        22.92        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 
       27.35        18.41        21.73        31.40        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-A19S 
        4.21        13.45        28.60        42.84        34.68        36.07 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG 
        6.58        17.72        78.44        11.80        13.08        12.62 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
        6.71         3.58         5.36        13.28         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        3.29        64.47        11.01        23.80        14.24        15.52 
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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       12.92        12.89        52.08         8.81        49.15         8.68 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FC 
        0.82         5.23         3.22         7.36        10.78         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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A 
        9.90         7.23        11.61        31.33        84.72        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB 
       14.70        11.84        10.65        14.50        14.50         0.43 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O 
        5.79        18.05         0.33         0.69       164.19         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       10.98       185.16        71.01        11.84         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
        7.10        21.07        13.12         3.72         3.42         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.96         1.94         6.18         4.70         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                         0.13                          0.13 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                       142.45                        185.16 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                        18.64                         13.45 
[1] "0.1 - 142.4 (18.6)" "0.1 - 185.2 (13.4)"
[1] "hr=" "1"  
D32V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(5Q31.3) MUTATED    55  64
  DEL PEAK 10(5Q31.3) WILD-TYPE 118 102
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                          119                           220 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                           64                           102 
$`DEL PEAK 10(5Q31.3) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JG 
       12.99        16.67        28.08        31.59        11.87       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
       12.10       171.58        66.08        58.06        86.93        24.53 
TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GI 
       45.30        22.62       125.79       135.75       137.92        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A1X3 
      228.99        95.24       161.00       151.53         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       11.34        11.11         9.90        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
      117.21        20.38       107.34        61.18        53.92       215.44 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       17.85        54.02        17.29        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29E 
       94.98         4.96       168.26        13.55        47.84        63.78 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       72.07        56.84        56.42        55.92        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       46.82        36.82        59.28        67.43       314.56       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT 
      208.04        48.72        89.33        75.48        14.30        44.88 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MP 
      129.27        28.83       103.20        96.23       167.90       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH 
       43.23       134.40       122.73         3.68        54.51       138.81 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A195 
       36.95        64.08        34.32       201.80       148.08        35.44 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NE 
        9.17        98.40       152.35        50.89        23.34        20.15 
TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZC 
       32.05       174.21        15.72        48.59        48.85       357.37 
TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 
       15.45       101.26       133.55        53.16        49.48        77.82 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
       28.73       174.84        26.73         2.04       139.89        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-A825 
       64.44        62.79        50.10        65.88       294.77        63.02 
TCGA-W3-A828 TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
      121.08        90.28        22.68        43.73        15.16 

$`DEL PEAK 10(5Q31.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH 
       23.77       115.53       168.00        86.76        62.07        42.08 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        59.57       130.72        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       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35       145.12        32.94        63.81        26.89 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      178.32        18.18       125.19        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       15.19       170.20        89.13       137.79        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG 
      117.17        54.67         3.65        22.29        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        68.25 
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       133.81       151.27        91.56        63.35        80.61 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       13.97        64.64         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 
      369.93       195.02       102.90        39.29        86.14        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       79.66        90.97       126.81        13.91        55.59        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       21.67        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MS 
       16.96       204.66       158.63       203.05        47.54       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
       71.21        53.26       124.31        51.62        13.81        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      172.18       127.20        53.19        27.35        51.35       109.58 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       31.40        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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       33.21         6.77        92.98       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       38.27        34.82        29.46        94.39       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD 
      202.65        20.91        28.08         7.79        27.72        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       40.27         9.70        32.75        47.38        23.93        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 
       11.41       148.80        26.56        27.09        27.02        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       66.67        12.43        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-A6C9 
       47.54         0.16        19.30         9.90         7.23        11.74 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
      117.93        84.72        32.48        39.58        46.36        12.62 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       21.37        59.41       357.04         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        0.69       212.22         4.01        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        38.56        54.38         8.61        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
       52.34         3.75         2.20        30.18        10.36        36.03 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                         2.04                          0.16 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                       357.37                        369.93 
  DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE 
                        54.51                         47.46 
[1] "2.0 - 357.4 (54.5)" "0.2 - 369.9 (47.5)"
[1] "hr=" "1"  
D32V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 10(5Q31.3) MUTATED                   22             2
  DEL PEAK 10(5Q31.3) WILD-TYPE                 39             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 10(5Q31.3) MUTATED                                          29
  DEL PEAK 10(5Q31.3) WILD-TYPE                                        43
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 10(5Q31.3) MUTATED                    71
  DEL PEAK 10(5Q31.3) WILD-TYPE                 138
D32V4, multiclass
                                           clus
vv                                          DEL PEAK 10(5Q31.3) MUTATED
  DISTANT METASTASIS                                                 22
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          29
  REGIONAL LYMPH NODE                                                71
                                           clus
vv                                          DEL PEAK 10(5Q31.3) WILD-TYPE
  DISTANT METASTASIS                                                   39
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            43
  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 10(5Q31.3) MUTATED             6       2      13        5        7
  DEL PEAK 10(5Q31.3) WILD-TYPE           6       5      15       12       20
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 10(5Q31.3) MUTATED          9         4         7         5
  DEL PEAK 10(5Q31.3) WILD-TYPE       13        10        12         7
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 10(5Q31.3) MUTATED          12          8         12         17
  DEL PEAK 10(5Q31.3) WILD-TYPE        23          7         20         41
                               vv
clus                            STAGE IV
  DEL PEAK 10(5Q31.3) MUTATED          5
  DEL PEAK 10(5Q31.3) WILD-TYPE       14
D32V5, multiclass
             clus
vv            DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  I OR II NOS                           6                             6
  STAGE 0                               2                             5
  STAGE I                              13                            15
  STAGE IA                              5                            12
  STAGE IB                              7                            20
  STAGE II                              9                            13
  STAGE IIA                             4                            10
  STAGE IIB                             7                            12
  STAGE IIC                             5                             7
  STAGE III                            12                            23
  STAGE IIIA                            8                             7
  STAGE IIIB                           12                            20
  STAGE IIIC                           17                            41
  STAGE IV                              5                            14
[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(5Q31.3) MUTATED      20 26 24 29
  DEL PEAK 10(5Q31.3) WILD-TYPE    43 45 50 38
D32V6, multiclass
       clus
vv      DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  T0+T1                          20                            43
  T2                             26                            45
  T3                             24                            50
  T4                             29                            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 10(5Q31.3) MUTATED    64  24  11  16
  DEL PEAK 10(5Q31.3) WILD-TYPE 104  37  27  31
D32V7, multiclass
    clus
vv   DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  N0                          64                           104
  N1                          24                            37
  N2                          11                            27
  N3                          16                            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 10(5Q31.3) MUTATED   111   0   1   2   3
  DEL PEAK 10(5Q31.3) WILD-TYPE 195   4   2   2   6
D32V8, multiclass
     clus
vv    DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  M0                          111                           195
  M1                            0                             4
  M1A                           1                             2
  M1B                           2                             2
  M1C                           3                             6
[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 10(5Q31.3) MUTATED   47 30
  DEL PEAK 10(5Q31.3) WILD-TYPE 82 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED     47   30
  DEL PEAK 10(5Q31.3) WILD-TYPE   82   57
     clus
vv    DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  NO                           47                            82
  YES                          30                            57
[1] 2 2
[1] FALSE
D32V10, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q31.3) MUTATED    10 114
  DEL PEAK 10(5Q31.3) WILD-TYPE  33 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED     10  114
  DEL PEAK 10(5Q31.3) WILD-TYPE   33  190
     clus
vv    DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  NO                           10                            33
  YES                         114                           190
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q31.3) MUTATED    49  75
  DEL PEAK 10(5Q31.3) WILD-TYPE  82 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED     49   75
  DEL PEAK 10(5Q31.3) WILD-TYPE   82  142
        clus
vv       DEL PEAK 10(5Q31.3) MUTATED DEL PEAK 10(5Q31.3) WILD-TYPE
  FEMALE                          49                            82
  MALE                            75                           142
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5Q31.3) MUTATED       2                         0   116
  DEL PEAK 10(5Q31.3) WILD-TYPE     3                         1   210
D32V13, multiclass
                           clus
vv                          DEL PEAK 10(5Q31.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             116
                           clus
vv                          DEL PEAK 10(5Q31.3) WILD-TYPE
  ASIAN                                                 3
  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"
D32V14, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q31.3) MUTATED     0 120
  DEL PEAK 10(5Q31.3) WILD-TYPE   7 214
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q31.3) MUTATED      0  120
  DEL PEAK 10(5Q31.3) WILD-TYPE    7  214
                        clus
vv                       DEL PEAK 10(5Q31.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                         120
                        clus
vv                       DEL PEAK 10(5Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           214
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 11(6Q22.31) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 11(6Q22.31) MUTATED    93 100
  DEL PEAK 11(6Q22.31) WILD-TYPE  75  65
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                           193                            140 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                           100                             65 
$`DEL PEAK 11(6Q22.31) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 
        3.02         6.97        16.47       111.09        32.42        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       10.29        85.32        68.22        86.76        11.41        44.19 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.16        92.42        56.19        64.44        59.57        15.25 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.00         6.31       103.59        26.37        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       54.74        54.31        21.44        25.78       110.24        52.01 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM 
       13.68        22.06        10.22         4.18        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
      124.47        87.62        21.93        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-A5UL 
        4.93         6.64         7.00        17.56        23.15        13.35 
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-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I 
       12.20         5.13         4.31        60.23         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        1.08        39.62         8.09         8.84         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GL 
        9.67        36.33        51.12        17.98        60.00        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       33.83        55.69         5.42        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
        2.70        47.51         2.73         7.96       125.65        26.99 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16        52.67         5.56       122.73        51.62         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JA 
       13.81        15.95         3.22        22.92        21.60        22.22 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B 
        0.95        21.73        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-A19T TCGA-ER-A2NE TCGA-ER-A2NF 
       42.84        34.68         9.57         6.58         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P 
       12.62         6.58        22.49         1.71         5.62        15.72 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
        3.58         2.20         4.70        64.47         3.45        23.80 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30         3.39        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-A1ZS 
       30.87        12.92        47.38         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 
       40.64         8.68        27.39         5.23         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       28.73        14.20         5.98         0.20         0.99         0.13 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
        7.23        31.33        16.24        15.42        12.16        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       10.65        14.50         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM 
        0.33         2.99        71.01        11.84         7.10        18.67 
TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
        3.72         1.94        12.07         6.18         4.70         6.67 
TCGA-Z2-AA3V 
        5.98 

$`DEL PEAK 11(6Q22.31) WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        6.97         8.52        70.16       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK 
       81.24         8.38        21.14        88.50         7.50         6.31 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3MO TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS 
        9.34        31.30        32.28        32.61        47.87        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GQ 
       23.11        29.72        15.19       142.45       108.79        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW 
        5.56        24.07         4.01         5.72         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-EE-A17X TCGA-EE-A17Z 
       13.15         0.20         0.13        19.00        11.57         6.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2GC 
        4.34        15.85        62.79         9.50        12.03        34.29 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR 
       47.21        30.08        19.43        16.01        28.31         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       13.02        34.98         6.18         9.53        29.46        44.25 
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-A3AA TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J8 
       60.49       124.31        30.15        12.72        21.60        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        18.41        31.40        12.95        38.40        76.41 
TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
        3.78        13.45        28.60        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A3YN TCGA-FR-A44A 
       11.80         1.87        11.74         9.04        18.41        85.74 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z3 
        6.71         5.36        13.28         3.29        11.01        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZY 
       15.52         7.33        19.53        12.89        52.08         0.82 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       53.85        10.78         6.41         2.27         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         0.85        11.61        44.28        84.72        10.13 
TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A694 TCGA-W3-A824 
       14.70        14.50        14.50        15.81         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 
        8.98        60.03        10.98       185.16         5.49         6.48 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       21.07        13.12         3.42        21.83         5.36         1.08 
TCGA-WE-AAA0 TCGA-Z2-A8RT 
       19.96         8.22 

  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                        125.65                         185.16 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                         13.35                          15.93 
[1] "0.1 - 125.7 (13.3)" "0.1 - 185.2 (15.9)"
[1] "hr=" "1.2"
D33V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 11(6Q22.31) MUTATED    96 101
  DEL PEAK 11(6Q22.31) WILD-TYPE  77  65
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                           197                            142 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                           101                             65 
$`DEL PEAK 11(6Q22.31) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 
       17.03        61.02        16.57       112.04       112.57        31.59 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       43.43       103.10       168.00        86.76        11.87        62.07 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       42.08       171.58        56.19        66.08        59.57        58.06 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53        13.87       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       55.73       145.12        22.62        26.89       125.79       135.75 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM 
      178.32        79.59        11.61        58.52        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      161.00       137.79       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 
       22.29        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-EB-A6L9 
       10.49       215.44        68.25        17.29        52.01        12.20 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       27.22        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.96       133.81       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       47.84        13.97        72.07        64.64         2.60        56.84 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       37.35        14.47        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       59.28       314.56       161.03        79.66        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       13.91        94.82        21.67       129.27        28.83        61.51 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      268.73        16.96       158.63       248.65       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       122.73        51.62         3.68        13.81        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH 
      172.18       127.20        64.08        53.19       201.80       109.58 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
      148.08        35.44         9.17        98.40        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P 
       26.37       268.93       152.35         6.44        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET 
       50.89         8.88        20.15        16.37        31.27        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC 
       46.98        33.21         6.77        15.72        15.16        34.82 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       29.46       216.92        48.59       202.65        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.02        50.14        66.67        28.73       174.84 
TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 
       26.73         0.20        22.92        47.54         7.23       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
       64.44        62.79        32.48        46.36        12.62        21.37 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-AA1O 
      357.04       294.77         6.67        18.05         0.33         4.01 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AAA3 
      105.04        24.03         8.61        90.28        52.34        10.36 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        14.43        93.07        11.74 

$`DEL PEAK 11(6Q22.31) WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       12.99        16.67        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK 
       95.74        65.49        23.77       115.53       113.52        12.10 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3MO TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS 
        9.34        56.35        32.94        63.81       137.92        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GQ 
      125.19        30.84        15.19       228.99       170.20        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      129.63       117.17        18.12        11.34        11.11         9.90 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 
       36.03        20.38       176.55       107.34        23.44        28.60 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5VV 
       15.68        13.87        10.16        17.85        54.02         6.35 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29N 
       29.82         8.65       151.27        91.56        63.78        18.61 
TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       56.42        67.43       208.04        48.72        89.33        54.74 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD 
       75.48        14.30        55.59        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       134.40       124.31        54.51       138.81 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 
       36.95        34.32        27.35        51.35        31.40        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19S 
       50.76        77.75        48.89       131.51        61.05        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NH TCGA-ER-A3ES 
      148.18        79.99        43.82        23.34        32.05       247.04 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE 
       92.98       174.21       210.08         7.00        38.27        94.39 
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-GF-A6C9 TCGA-GN-A262 
        0.16        19.30         9.90         2.04        11.74       139.89 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH 
       84.72        10.13        39.58        50.10        59.41        65.88 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W 
        0.69       212.22        63.02       121.08        42.08       219.16 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
       38.56        54.38        56.98        59.41         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-A8RT 
       43.73         2.20        30.18        23.64 

  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                          0.20                           0.16 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                        369.93                         247.04 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                         51.62                          49.17 
[1] "0.2 - 369.9 (51.6)" "0.2 - 247.0 (49.2)"
[1] "hr=" "1"  
D33V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 11(6Q22.31) MUTATED                   36             4
  DEL PEAK 11(6Q22.31) WILD-TYPE                 25             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 11(6Q22.31) MUTATED                                          44
  DEL PEAK 11(6Q22.31) WILD-TYPE                                        28
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 11(6Q22.31) MUTATED                   118
  DEL PEAK 11(6Q22.31) WILD-TYPE                  91
D33V4, multiclass
                                           clus
vv                                          DEL PEAK 11(6Q22.31) MUTATED
  DISTANT METASTASIS                                                  36
  PRIMARY TUMOR                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           44
  REGIONAL LYMPH NODE                                                118
                                           clus
vv                                          DEL PEAK 11(6Q22.31) WILD-TYPE
  DISTANT METASTASIS                                                    25
  PRIMARY TUMOR                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             28
  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
  DEL PEAK 11(6Q22.31) MUTATED             8       4      15       10       17
  DEL PEAK 11(6Q22.31) WILD-TYPE           4       3      13        7       10
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 11(6Q22.31) MUTATED          8         8         9         6
  DEL PEAK 11(6Q22.31) WILD-TYPE       14         6        10         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 11(6Q22.31) MUTATED          21          9         18         39
  DEL PEAK 11(6Q22.31) WILD-TYPE        14          6         14         19
                                vv
clus                             STAGE IV
  DEL PEAK 11(6Q22.31) MUTATED          8
  DEL PEAK 11(6Q22.31) WILD-TYPE       11
D33V5, multiclass
             clus
vv            DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  I OR II NOS                            8                              4
  STAGE 0                                4                              3
  STAGE I                               15                             13
  STAGE IA                              10                              7
  STAGE IB                              17                             10
  STAGE II                               8                             14
  STAGE IIA                              8                              6
  STAGE IIB                              9                             10
  STAGE IIC                              6                              6
  STAGE III                             21                             14
  STAGE IIIA                             9                              6
  STAGE IIIB                            18                             14
  STAGE IIIC                            39                             19
  STAGE IV                               8                             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 11(6Q22.31) MUTATED      36 45 36 38
  DEL PEAK 11(6Q22.31) WILD-TYPE    27 26 38 29
D33V6, multiclass
       clus
vv      DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  T0+T1                           36                             27
  T2                              45                             26
  T3                              36                             38
  T4                              38                             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 11(6Q22.31) MUTATED   95 37 23 30
  DEL PEAK 11(6Q22.31) WILD-TYPE 73 24 15 17
D33V7, multiclass
    clus
vv   DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  N0                           95                             73
  N1                           37                             24
  N2                           23                             15
  N3                           30                             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 11(6Q22.31) MUTATED   183   2   2   1   4
  DEL PEAK 11(6Q22.31) WILD-TYPE 123   2   1   3   5
D33V8, multiclass
     clus
vv    DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  M0                           183                            123
  M1                             2                              2
  M1A                            2                              1
  M1B                            1                              3
  M1C                            4                              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"
D33V9, binary
                                cls
clus                              0  1
  DEL PEAK 11(6Q22.31) MUTATED   68 57
  DEL PEAK 11(6Q22.31) WILD-TYPE 61 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED     68   57
  DEL PEAK 11(6Q22.31) WILD-TYPE   61   30
     clus
vv    DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  NO                            68                             61
  YES                           57                             30
[1] 2 2
[1] FALSE
D33V10, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED    27 174
  DEL PEAK 11(6Q22.31) WILD-TYPE  16 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED     27  174
  DEL PEAK 11(6Q22.31) WILD-TYPE   16  130
     clus
vv    DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  NO                            27                             16
  YES                          174                            130
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED    82 120
  DEL PEAK 11(6Q22.31) WILD-TYPE  49  97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED     82  120
  DEL PEAK 11(6Q22.31) WILD-TYPE   49   97
        clus
vv       DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  FEMALE                           82                             49
  MALE                            120                             97
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q22.31) MUTATED       2                         1   191
  DEL PEAK 11(6Q22.31) WILD-TYPE     3                         0   135
D33V13, multiclass
                           clus
vv                          DEL PEAK 11(6Q22.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              191
                           clus
vv                          DEL PEAK 11(6Q22.31) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                135
[1] 3 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 11(6Q22.31) MUTATED     3 194
  DEL PEAK 11(6Q22.31) WILD-TYPE   4 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      3  194
  DEL PEAK 11(6Q22.31) WILD-TYPE    4  140
                        clus
vv                       DEL PEAK 11(6Q22.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          194
                        clus
vv                       DEL PEAK 11(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            140
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 12(6Q26) MUTATION ANALYSIS
D34V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q26) MUTATED    94 106
  DEL PEAK 12(6Q26) WILD-TYPE  74  59
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        200                         133 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        106                          59 
$`DEL PEAK 12(6Q26) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 
        3.02         6.97        16.47       111.09        32.42        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       10.29        85.32        68.22        86.76        11.41        44.19 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.16        92.42        56.19        64.44        59.57        15.25 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       13.32        24.00         6.31       103.59        26.37        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
       93.21        54.74        54.31        32.28        21.44        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      110.24        52.01        13.68        23.11        22.06        10.22 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
        4.18        38.93        75.65       124.47        87.62         5.56 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       21.93        11.31        13.22        14.60        48.79        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       39.19         9.99        36.69        25.15         4.93         6.64 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y 
        7.00        17.56        23.15        13.35        13.22        10.55 
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-A29A TCGA-EE-A29B TCGA-EE-A29C 
       60.23         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q 
       11.15         8.55        36.85         1.08        39.62         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.84         9.99        30.44         2.43        32.15         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       60.00        35.54        33.83        55.69         5.42        13.02 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF 
       36.33         8.84        98.27         2.70        47.51         2.73 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
        7.96       125.65        26.99        53.16        52.67         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
      122.73        51.62         3.68        13.81        15.95         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       22.92        21.60        22.22         0.95        21.73        33.60 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       18.61        12.95         5.72        25.18         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P 
       11.11       114.15        34.88         4.21        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE 
        9.57        36.07         6.58        17.72         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P 
       13.08        12.62        22.49         1.71         5.62        15.72 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
        3.58         2.20         4.70        64.47         3.45        23.80 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30         3.39        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-A1ZS 
       30.87        12.92        47.38         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 
       40.64         8.68        27.39         0.82         5.23         3.22 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       28.73        14.20         5.98         0.20         0.99         0.13 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
        7.23        31.33        16.24        15.42        12.16        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       10.65        14.50        14.50         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       18.05         0.33         2.99        71.01        11.84         5.49 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        7.10        18.67         3.72         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-AA3V 
        4.70         5.98 

$`DEL PEAK 12(6Q26) WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        6.97         8.52        70.16       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK 
       81.24         8.38        21.14        88.50         7.50         6.31 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MO 
      114.67        46.98        46.32        82.29        61.38         9.34 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE 
       31.30        32.61        47.87        17.72        29.72        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      142.45       108.79        11.44        24.07         4.01         5.72 
TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB 
        9.90        35.80        10.03        13.68        44.52        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       19.36        14.83        13.15         0.20         0.13        19.00 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29E 
        0.20        11.57         6.31         4.34        15.85        62.79 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI 
        9.50        12.03        11.31        34.29        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M8 
       19.43        16.01        28.31         1.15        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        60.49       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        18.41        31.40 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A1A1 
       38.40        76.41         3.78        13.45        28.60        78.44 
TCGA-ER-A2NC TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A 
       11.80        11.74         9.04         6.58        18.41        85.74 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z3 
        6.71         5.36        13.28         3.29        11.01        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A4F0 
       15.52         7.33        19.53        12.89        52.08        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
        7.36        10.78         6.41         2.27         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         0.85        11.61        44.28        84.72        10.13 
TCGA-GN-A26D TCGA-GN-A8LK TCGA-HR-A2OH TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       14.70        14.50        15.81         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       60.03        10.98       185.16         6.48        21.07        13.12 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-A8RT 
        3.42        21.83         5.36         1.08        19.96         8.22 
TCGA-Z2-AA3S 
        6.67 

  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                       0.13                        0.13 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     125.65                      185.16 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     13.745                      15.850 
[1] "0.1 - 125.7 (13.7)" "0.1 - 185.2 (15.8)"
[1] "hr=" "1.3"
D34V2, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q26) MUTATED    97 107
  DEL PEAK 12(6Q26) WILD-TYPE  76  59
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        204                         135 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                        107                          59 
$`DEL PEAK 12(6Q26) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 
       17.03        61.02        16.57       112.04       112.57        31.59 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       43.43       103.10       168.00        86.76        11.87        62.07 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       42.08       171.58        56.19        66.08        59.57        58.06 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        24.53        13.87       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
      174.84        55.73       145.12        32.94        22.62        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
      125.79       135.75       178.32       125.19        79.59        11.61 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
       58.52        89.13        95.24       161.00       137.79       129.63 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA 
      151.53        54.67         3.65         6.41        22.29        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       66.25        22.95        48.89       117.21       194.83        35.93 
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-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       68.25        17.29        52.01        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       133.81       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 
       64.64         2.60        56.84        37.35        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
      369.93        25.87       195.02        17.92       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GL 
       39.29        86.14        59.28       314.56       161.03        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97       126.81        13.91        55.59        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK 
      129.27        28.83        61.51       268.73        16.96       158.63 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      248.65       162.48        71.21        53.26       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        3.68        13.81        23.47       172.18       127.20        64.08 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19       201.80       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
        8.88       148.18        23.34        20.15        16.37        31.27 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC 
       46.98        33.21         6.77        15.72        15.16        34.82 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       29.46       216.92        48.59       202.65        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.09        27.02        50.14        28.73       174.84 
TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 
       26.73         0.20        22.92        47.54         7.23       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
       64.44        62.79        32.48        46.36        12.62        21.37 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41       357.04       294.77         6.67        18.05         0.33 
TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
        4.01       105.04        24.03        38.56         8.61        90.28 
TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3V 
       52.34        10.36        15.16        36.03        14.43        11.74 

$`DEL PEAK 12(6Q26) WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       12.99        16.67        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK 
       95.74        65.49        23.77       115.53       113.52        12.10 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MO 
      130.72        46.98        46.32       166.52        86.93         9.34 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE 
       56.35        63.81       137.92        18.18        30.84        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A1X3 TCGA-D9-A3Z1 
      228.99       170.20        29.06       117.17        18.12        11.34 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 
       11.11         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-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C 
       54.02         6.35        12.20        29.82         8.65       151.27 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2GC 
       91.56        63.78        18.61        56.42        46.82        67.43 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR 
      208.04        48.72        89.33        54.74        75.48        14.30 
TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
       44.88        19.76        47.28       103.27       103.20       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       134.40 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD 
      124.31        54.51       138.81        36.95        34.32        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19L 
       51.35        31.40        50.76        77.75        48.89       131.51 
TCGA-ER-A19M TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       61.05        79.99        43.82        32.05       247.04        80.32 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE 
       92.98       174.21       210.08         7.00        38.27        94.39 
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-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       74.73        77.82        66.67        12.43        49.45        77.88 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
        0.16        19.30         9.90         2.04        11.74       139.89 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A8LK TCGA-HR-A2OH TCGA-RP-A694 
       84.72        10.13        39.58        50.10        65.88         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K5 
      212.22        63.02       121.08        42.08       219.16        54.38 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       56.98        59.41         3.75        22.68        43.73         2.20 
TCGA-WE-AAA0 TCGA-Z2-A8RT TCGA-Z2-AA3S 
       30.18        23.64        93.07 

  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                       0.20                        0.16 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     369.93                      247.04 
  DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE 
                     51.255                      49.450 
[1] "0.2 - 369.9 (51.3)" "0.2 - 247.0 (49.5)"
[1] "hr=" "1.1"
D34V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 12(6Q26) MUTATED                   39             4
  DEL PEAK 12(6Q26) WILD-TYPE                 22             1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 12(6Q26) MUTATED                                          45
  DEL PEAK 12(6Q26) WILD-TYPE                                        27
                             vv
clus                          REGIONAL LYMPH NODE
  DEL PEAK 12(6Q26) MUTATED                   120
  DEL PEAK 12(6Q26) WILD-TYPE                  89
D34V4, multiclass
                                           clus
vv                                          DEL PEAK 12(6Q26) MUTATED
  DISTANT METASTASIS                                               39
  PRIMARY TUMOR                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        45
  REGIONAL LYMPH NODE                                             120
                                           clus
vv                                          DEL PEAK 12(6Q26) WILD-TYPE
  DISTANT METASTASIS                                                 22
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          27
  REGIONAL LYMPH NODE                                                89
[1] 4 2
[1] 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(6Q26) MUTATED             8       5      15       10       19
  DEL PEAK 12(6Q26) WILD-TYPE           4       2      13        7        8
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 12(6Q26) MUTATED          8         6        10         6        22
  DEL PEAK 12(6Q26) WILD-TYPE       14         8         9         6        13
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 12(6Q26) MUTATED            8         20         40        8
  DEL PEAK 12(6Q26) WILD-TYPE          7         12         18       11
D34V5, multiclass
             clus
vv            DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  I OR II NOS                         8                           4
  STAGE 0                             5                           2
  STAGE I                            15                          13
  STAGE IA                           10                           7
  STAGE IB                           19                           8
  STAGE II                            8                          14
  STAGE IIA                           6                           8
  STAGE IIB                          10                           9
  STAGE IIC                           6                           6
  STAGE III                          22                          13
  STAGE IIIA                          8                           7
  STAGE IIIB                         20                          12
  STAGE IIIC                         40                          18
  STAGE IV                            8                          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 12(6Q26) MUTATED      39 45 36 39
  DEL PEAK 12(6Q26) WILD-TYPE    24 26 38 28
D34V6, multiclass
       clus
vv      DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  T0+T1                        39                          24
  T2                           45                          26
  T3                           36                          38
  T4                           39                          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
  DEL PEAK 12(6Q26) MUTATED   96 38 24 31
  DEL PEAK 12(6Q26) WILD-TYPE 72 23 14 16
D34V7, multiclass
    clus
vv   DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  N0                        96                          72
  N1                        38                          23
  N2                        24                          14
  N3                        31                          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 12(6Q26) MUTATED   188   2   2   1   4
  DEL PEAK 12(6Q26) WILD-TYPE 118   2   1   3   5
D34V8, multiclass
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  M0                        188                         118
  M1                          2                           2
  M1A                         2                           1
  M1B                         1                           3
  M1C                         4                           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"
D34V9, binary
                             cls
clus                           0  1
  DEL PEAK 12(6Q26) MUTATED   71 58
  DEL PEAK 12(6Q26) WILD-TYPE 58 29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     71   58
  DEL PEAK 12(6Q26) WILD-TYPE   58   29
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  NO                         71                          58
  YES                        58                          29
[1] 2 2
[1] FALSE
D34V10, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    29 179
  DEL PEAK 12(6Q26) WILD-TYPE  14 125
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     29  179
  DEL PEAK 12(6Q26) WILD-TYPE   14  125
     clus
vv    DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  NO                         29                          14
  YES                       179                         125
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q26) MUTATED    88 121
  DEL PEAK 12(6Q26) WILD-TYPE  43  96
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED     88  121
  DEL PEAK 12(6Q26) WILD-TYPE   43   96
        clus
vv       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  FEMALE                        88                          43
  MALE                         121                          96
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q26) MUTATED       1                         1   199
  DEL PEAK 12(6Q26) WILD-TYPE     4                         0   127
D34V13, multiclass
                           clus
vv                          DEL PEAK 12(6Q26) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                           199
                           clus
vv                          DEL PEAK 12(6Q26) WILD-TYPE
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             127
[1] 3 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 12(6Q26) MUTATED     4 201
  DEL PEAK 12(6Q26) WILD-TYPE   3 133
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q26) MUTATED      4  201
  DEL PEAK 12(6Q26) WILD-TYPE    3  133
                        clus
vv                       DEL PEAK 12(6Q26) MUTATED DEL PEAK 12(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       201                         133
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 13(8P23.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(8P23.3) MUTATED    37  43
  DEL PEAK 13(8P23.3) WILD-TYPE 131 122
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           80                           253 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           43                           122 
$`DEL PEAK 13(8P23.3) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JD 
        6.97        16.47        22.55        10.29        88.50        11.41 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MO 
        7.50        92.42        64.44        15.25        46.98         9.34 
TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM 
       21.44        52.01        17.72        22.06        10.22        75.65 
TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C 
        4.93         7.00         0.20        12.20         4.34        37.97 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 
       36.85         1.08        39.62         2.43        36.30         9.67 
TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       30.08        13.02         2.73        44.25         7.96        14.56 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
       56.02        25.08        26.99        53.16         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 
       51.62        15.95         3.22        33.60        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19J TCGA-ER-A19S TCGA-ER-A19T 
        5.72         3.78        11.90         4.21        36.07         6.58 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A8YC TCGA-FS-A1YY 
        1.87        13.08         1.71         5.62         2.20        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A4FD 
       23.80         7.30        20.38        12.92        40.64         2.27 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
        0.99        31.33        84.72        11.05         5.79        18.05 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 
       10.98        11.84         7.10         5.36        19.96         1.94 
TCGA-YG-AA3P TCGA-Z2-AA3S 
        4.70         6.67 

$`DEL PEAK 13(8P23.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         8.52       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      110.79        28.08        45.83        81.24        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       21.14        68.22        86.76        44.19        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       56.19        59.57       114.67        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       13.32        24.00         6.31       103.59        26.37        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       93.21        54.74        31.30        54.31        32.28        32.61 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB 
       25.78       110.24        47.87        13.68        23.11        29.72 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       15.19         4.18       142.45       108.79        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        5.72         9.90        11.31        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-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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.12         1.12         1.35         5.13         4.31        60.23 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       15.85         9.21         1.18         7.99         9.90        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       62.79         8.55         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99        30.44        32.15         8.09        11.31        49.22 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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        55.69 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        5.42         1.15        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-A2MJ 
        2.70         6.18        47.51         9.53        29.46        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
      125.65       111.91        21.60        60.49        52.67       124.31 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        30.15        13.81        12.72        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       21.73        31.40        18.61        76.41        25.18         3.52 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.11       114.15        34.88        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-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       12.62        11.74         9.04         6.58        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       85.74        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.70         3.29        64.47         3.45        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.33         3.39         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.89        47.38        52.08         8.65         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-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-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.20         0.13         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 
        7.23         0.85        11.61        44.28        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       15.42        12.16        14.70        11.84        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-RP-A693 TCGA-RP-A694 
       14.50        14.50        15.81         0.43         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 
      164.19         8.98        60.03         2.99       185.16        71.01 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        5.49         6.48        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT 
        3.42        21.83         1.08        12.07         6.18         8.22 
TCGA-Z2-AA3V 
        5.98 

  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                         0.20                          0.13 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                       122.73                        185.16 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                        12.56                         15.72 
[1] "0.2 - 122.7 (12.6)" "0.1 - 185.2 (15.7)"
[1] "hr=" "1.3"
D35V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(8P23.3) MUTATED    39  43
  DEL PEAK 13(8P23.3) WILD-TYPE 134 123
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           82                           257 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                           43                           123 
$`DEL PEAK 13(8P23.3) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JD 
       61.02        16.57        31.59        43.43       115.53        11.87 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MO 
      113.52       171.58        66.08        58.06        46.98         9.34 
TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GM 
       22.62       135.75        18.18        79.59        11.61        95.24 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A6L9 TCGA-EE-A183 
      151.53         3.65        65.92        10.49        12.20        26.89 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V 
      151.27        47.84        64.64         2.60        56.84        25.87 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MG 
       36.82        39.29        48.72        55.59       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
       16.96       204.66       167.90        47.54       248.65       162.48 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JI 
       53.26       122.73        51.62        23.47       172.18       148.08 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19J 
       13.94        50.76         9.17        48.89        13.02         6.44 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3PL TCGA-ER-A42K 
       37.25         8.88        23.34        16.37        33.21         6.77 
TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZJ 
       34.82       228.59       202.65        27.72       357.37        47.38 
TCGA-FS-A1ZT TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-OD-A75X 
       53.16        77.88        22.92       117.93        84.72       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZY 
        6.67        18.05        42.08        24.03         8.61        43.73 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3P TCGA-Z2-AA3S 
       30.18        10.36        14.43        93.07 

$`DEL PEAK 13(8P23.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        12.99        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       168.00        86.76        62.07        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       56.19        59.57       130.72        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        24.53        13.87       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      174.84        55.73        56.35       145.12        32.94        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB 
       26.89       125.79       137.92       178.32       125.19        30.84 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       15.19        58.52       228.99       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX 
      137.79        29.06       129.63       117.17        54.67         6.41 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       18.12        11.34        22.29        11.11         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-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-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60       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        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        6.35        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       14.70        68.15         4.96       133.81        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        80.61        13.97        63.78        72.07 
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       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02        17.92        46.82       102.90        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       161.03       208.04        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       126.81        13.91        14.30 
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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       61.51        47.28       103.27        96.23       158.63       203.05 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE 
       43.23       134.40        71.21       124.31         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       53.19       201.80        27.35        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       35.44        77.75        98.40        12.59        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18        79.99        43.82        20.15        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
      247.04        80.32        46.98        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
      210.08        15.16         7.00        38.27        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      216.92        48.59        20.91        28.08         7.79        48.85 
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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        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-FW-A3I3 
       28.73       174.84        12.43        26.73        49.45         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       11.74       139.89        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       39.58        46.36        12.62        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       65.88       357.04         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
      121.08         4.01       219.16       105.04        38.56        54.38 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       90.28        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
        2.20        15.16        36.03        23.64        11.74 

  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                         2.60                          0.16 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                       357.37                        369.93 
  DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE 
                        47.18                         53.19 
[1] "2.6 - 357.4 (47.2)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.1"
D35V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 13(8P23.3) MUTATED                   13             2
  DEL PEAK 13(8P23.3) WILD-TYPE                 48             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 13(8P23.3) MUTATED                                          11
  DEL PEAK 13(8P23.3) WILD-TYPE                                        61
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 13(8P23.3) MUTATED                    55
  DEL PEAK 13(8P23.3) WILD-TYPE                 154
D35V4, multiclass
                                           clus
vv                                          DEL PEAK 13(8P23.3) MUTATED
  DISTANT METASTASIS                                                 13
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          11
  REGIONAL LYMPH NODE                                                55
                                           clus
vv                                          DEL PEAK 13(8P23.3) WILD-TYPE
  DISTANT METASTASIS                                                   48
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            61
  REGIONAL LYMPH NODE                                                 154
[1] 4 2
[1] 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(8P23.3) MUTATED             2       2       9        6        7
  DEL PEAK 13(8P23.3) WILD-TYPE          10       5      19       11       20
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 13(8P23.3) MUTATED          2         3         5         0
  DEL PEAK 13(8P23.3) WILD-TYPE       20        11        14        12
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 13(8P23.3) MUTATED           8          2          7         17
  DEL PEAK 13(8P23.3) WILD-TYPE        27         13         25         41
                               vv
clus                            STAGE IV
  DEL PEAK 13(8P23.3) MUTATED          5
  DEL PEAK 13(8P23.3) WILD-TYPE       14
D35V5, multiclass
             clus
vv            DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  I OR II NOS                           2                            10
  STAGE 0                               2                             5
  STAGE I                               9                            19
  STAGE IA                              6                            11
  STAGE IB                              7                            20
  STAGE II                              2                            20
  STAGE IIA                             3                            11
  STAGE IIB                             5                            14
  STAGE IIC                             0                            12
  STAGE III                             8                            27
  STAGE IIIA                            2                            13
  STAGE IIIB                            7                            25
  STAGE IIIC                           17                            41
  STAGE IV                              5                            14
[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(8P23.3) MUTATED      18 20 10 16
  DEL PEAK 13(8P23.3) WILD-TYPE    45 51 64 51
D35V6, multiclass
       clus
vv      DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  T0+T1                          18                            45
  T2                             20                            51
  T3                             10                            64
  T4                             16                            51
[1] 4 2
[1] 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(8P23.3) MUTATED    35  12  10  17
  DEL PEAK 13(8P23.3) WILD-TYPE 133  49  28  30
D35V7, multiclass
    clus
vv   DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  N0                          35                           133
  N1                          12                            49
  N2                          10                            28
  N3                          17                            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 13(8P23.3) MUTATED    73   1   2   1   2
  DEL PEAK 13(8P23.3) WILD-TYPE 233   3   1   3   7
D35V8, multiclass
     clus
vv    DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  M0                           73                           233
  M1                            1                             3
  M1A                           2                             1
  M1B                           1                             3
  M1C                           2                             7
[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 13(8P23.3) MUTATED   32 21
  DEL PEAK 13(8P23.3) WILD-TYPE 97 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED     32   21
  DEL PEAK 13(8P23.3) WILD-TYPE   97   66
     clus
vv    DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  NO                           32                            97
  YES                          21                            66
[1] 2 2
[1] FALSE
D35V10, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.3) MUTATED    12  69
  DEL PEAK 13(8P23.3) WILD-TYPE  31 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED     12   69
  DEL PEAK 13(8P23.3) WILD-TYPE   31  235
     clus
vv    DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  NO                           12                            31
  YES                          69                           235
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, binary
                               cls
clus                              0   1
  DEL PEAK 13(8P23.3) MUTATED    28  54
  DEL PEAK 13(8P23.3) WILD-TYPE 103 163
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED     28   54
  DEL PEAK 13(8P23.3) WILD-TYPE  103  163
        clus
vv       DEL PEAK 13(8P23.3) MUTATED DEL PEAK 13(8P23.3) WILD-TYPE
  FEMALE                          28                           103
  MALE                            54                           163
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(8P23.3) MUTATED       1                         0    76
  DEL PEAK 13(8P23.3) WILD-TYPE     4                         1   250
D35V13, multiclass
                           clus
vv                          DEL PEAK 13(8P23.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              76
                           clus
vv                          DEL PEAK 13(8P23.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               250
[1] 3 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 13(8P23.3) MUTATED     1  80
  DEL PEAK 13(8P23.3) WILD-TYPE   6 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.3) MUTATED      1   80
  DEL PEAK 13(8P23.3) WILD-TYPE    6  254
                        clus
vv                       DEL PEAK 13(8P23.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          80
                        clus
vv                       DEL PEAK 13(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           254
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 14(9P23) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(9P23) MUTATED   106 121
  DEL PEAK 14(9P23) WILD-TYPE  62  44
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        227                         106 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        121                          44 
$`DEL PEAK 14(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        44.19         6.31        92.42        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       59.57        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        29.23        93.21        54.31 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        25.78       110.24        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GN 
       23.11        29.72        22.06         4.18        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
       87.62        24.07         4.01        21.93         5.72         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       11.31        14.60        48.79        35.80        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       13.68         9.99        44.52        25.15         4.93         6.64 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
        7.00        13.15         0.20        23.15        13.35        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
       11.57        10.55         8.12         1.12         1.35         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C 
       60.23         4.34        15.85         9.21         1.18        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        62.79         8.55         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.09         9.99        30.44         2.43        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       11.31         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       60.00        47.21        30.08        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
       55.69         5.42         1.15        13.02        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       98.27         6.18         9.53         2.73         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
      125.65       111.91        56.02        25.08        26.99        60.49 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.16       124.31       122.73         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       15.95        12.72         3.22        21.60        16.14        22.22 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.95        21.73        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-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       36.07         6.58        17.72         1.87         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       11.74         9.04        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YE 
       85.74        15.72         6.71         3.58         2.20         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       64.47         3.45        11.01        14.24         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
        3.39        20.38         8.22        11.08        30.87        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        49.15        40.64        27.39         0.82 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         3.22         7.36        28.73        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
        6.41         0.99         0.13         0.16         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       11.61        31.33        15.42        12.16        14.70        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        14.50        15.81        11.05         5.79 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.33         0.69         8.98        60.03         2.99        10.98 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       71.01        11.84         6.48         7.10        18.67        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 
       13.12         3.72        21.83         5.36         1.08         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         8.22         6.67         5.98 

$`DEL PEAK 14(9P23) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
        3.02         6.97         6.97         8.52       110.79        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       45.83        81.24         8.38        21.14        88.50        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 
       11.41         7.50        36.16        64.44       114.67        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
       82.29        13.32        54.74        31.30        32.28        32.61 
TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
       52.01        10.22        15.19       142.45       108.79        75.65 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB 
       11.44         5.56        13.22        10.03        36.69        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A6L9 
       19.36        17.56        14.83         0.13        19.00         0.20 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H 
        6.31        12.20         5.13         7.99         9.90        36.85 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.62         8.84        49.22        36.30        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-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 
       21.60        52.67         5.56        51.62        22.92        21.60 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19J 
       27.35        18.41        38.40        76.41       114.15         4.21 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FR-A7UA 
       78.44        11.80        13.08         6.58         5.36        13.28 
TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        4.70        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        17.33         9.90        44.28        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-AA1W 
       16.24        11.84         0.43        18.05       164.19       185.16 
TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-YG-AA3P 
        5.49         3.42        19.96         4.70 

  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                       0.13                        0.13 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                     125.65                      185.16 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                      13.68                       18.23 
[1] "0.1 - 125.7 (13.7)" "0.1 - 185.2 (18.2)"
[1] "hr=" "1.5"
D36V2, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(9P23) MUTATED   107 122
  DEL PEAK 14(9P23) WILD-TYPE  66  44
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        229                         110 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                        122                          44 
$`DEL PEAK 14(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        62.07        12.10       171.58        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       59.57        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        45.30       174.84       145.12 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        26.89       125.79       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GN 
      125.19        30.84        79.59        58.52        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      137.79       117.17        54.67         6.41        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       11.11         9.90        25.18        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
      117.21       194.83       176.55        35.93       107.34        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       65.92        68.09        10.49        13.87        10.16        68.25 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       17.29        52.01        29.82        27.22        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       14.70         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       13.55        47.84        13.97        63.78        72.07         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        37.35        55.92       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02        17.92        46.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL 
       67.43       314.56       161.03       208.04        48.72        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       126.81        13.91        14.30        55.59 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF 
       94.82        21.67       129.27        19.76        47.28       268.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       158.63       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      248.65       134.40       162.48       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       54.51        13.81        23.47       138.81       172.18        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        53.19       201.80       109.58       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       35.44        13.94         9.17        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       13.02        26.37       152.35       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND 
      162.08        50.89        37.25         8.88       148.18        23.34 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       20.15        31.27        32.05       247.04        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       210.08        15.16 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       34.82        94.39       216.92        48.59       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-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       32.75       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-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       12.43        26.73        49.45        22.92        47.54         0.16 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26A 
        7.23         2.04        11.74       117.93        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       39.58        12.62        50.10        21.37        59.41        65.88 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 
      294.77         6.67         0.33         0.69        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
        4.01        42.08       105.04        24.03        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY 
       90.28        56.98        59.41        52.34        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
        2.20        10.36        15.16        36.03        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

$`DEL PEAK 14(9P23) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       17.03        61.02        12.99        16.67       133.25        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       90.90        95.74        65.49        23.77       115.53        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 
       11.87       113.52        42.08        66.08       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
      166.52        60.23        55.73        56.35        32.94        63.81 
TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
      135.75        11.61        15.19       228.99       170.20        95.24 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A6EC 
       29.06       129.63       151.53         3.65        18.12        66.25 
TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       20.38        61.18        23.44        28.60       215.44        15.68 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A183 
       17.85        54.02         6.35        12.20         8.65        26.89 
TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R 
       68.15        63.35        80.61        64.64        56.84        14.47 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M7 
      102.90        36.82        89.33        54.74        44.88        28.83 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT 
       61.51       103.27       103.20        96.23        43.23        71.21 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE 
       53.26        51.62       127.20        36.95        27.35        51.35 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.76        77.75       268.93         6.44        79.99        43.82 
TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 
       16.37        80.32         7.00        38.27        29.46       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       28.08        40.27         9.70        47.38        23.93        74.73 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A5DY 
       26.56        27.02       174.84        77.88         0.20        19.30 
TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 
        9.90       139.89        84.72        10.13        64.44        46.36 
TCGA-LH-A9QB TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT 
      357.04        18.05       212.22       219.16        38.56         3.75 
TCGA-WE-AAA0 TCGA-YG-AA3P 
       30.18        14.43 

  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                       0.16                        0.20 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                     369.93                      357.04 
  DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE 
                     49.480                      51.485 
[1] "0.2 - 369.9 (49.5)" "0.2 - 357.0 (51.5)"
[1] "hr=" "1.3"
D36V3, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 14(9P23) MUTATED                   41             3
  DEL PEAK 14(9P23) WILD-TYPE                 20             2
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 14(9P23) MUTATED                                          52
  DEL PEAK 14(9P23) WILD-TYPE                                        20
                             vv
clus                          REGIONAL LYMPH NODE
  DEL PEAK 14(9P23) MUTATED                   140
  DEL PEAK 14(9P23) WILD-TYPE                  69
D36V4, multiclass
                                           clus
vv                                          DEL PEAK 14(9P23) MUTATED
  DISTANT METASTASIS                                               41
  PRIMARY TUMOR                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                        52
  REGIONAL LYMPH NODE                                             140
                                           clus
vv                                          DEL PEAK 14(9P23) WILD-TYPE
  DISTANT METASTASIS                                                 20
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          20
  REGIONAL LYMPH NODE                                                69
[1] 4 2
[1] 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(9P23) MUTATED            11       4      19       11       17
  DEL PEAK 14(9P23) WILD-TYPE           1       3       9        6       10
                             vv
clus                          STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 14(9P23) MUTATED         15        10        13         8        25
  DEL PEAK 14(9P23) WILD-TYPE        7         4         6         4        10
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 14(9P23) MUTATED            7         25         38       13
  DEL PEAK 14(9P23) WILD-TYPE          8          7         20        6
D36V5, multiclass
             clus
vv            DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  I OR II NOS                        11                           1
  STAGE 0                             4                           3
  STAGE I                            19                           9
  STAGE IA                           11                           6
  STAGE IB                           17                          10
  STAGE II                           15                           7
  STAGE IIA                          10                           4
  STAGE IIB                          13                           6
  STAGE IIC                           8                           4
  STAGE III                          25                          10
  STAGE IIIA                          7                           8
  STAGE IIIB                         25                           7
  STAGE IIIC                         38                          20
  STAGE IV                           13                           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 14(9P23) MUTATED      42 51 49 43
  DEL PEAK 14(9P23) WILD-TYPE    21 20 25 24
D36V6, multiclass
       clus
vv      DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  T0+T1                        42                          21
  T2                           51                          20
  T3                           49                          25
  T4                           43                          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
  DEL PEAK 14(9P23) MUTATED   114  43  24  30
  DEL PEAK 14(9P23) WILD-TYPE  54  18  14  17
D36V7, multiclass
    clus
vv   DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  N0                       114                          54
  N1                        43                          18
  N2                        24                          14
  N3                        30                          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 14(9P23) MUTATED   209   1   2   1   9
  DEL PEAK 14(9P23) WILD-TYPE  97   3   1   3   0
D36V8, multiclass
     clus
vv    DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  M0                        209                          97
  M1                          1                           3
  M1A                         2                           1
  M1B                         1                           3
  M1C                         9                           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 14(9P23) MUTATED   88 56
  DEL PEAK 14(9P23) WILD-TYPE 41 31
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED     88   56
  DEL PEAK 14(9P23) WILD-TYPE   41   31
     clus
vv    DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  NO                         88                          41
  YES                        56                          31
[1] 2 2
[1] FALSE
D36V10, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED    29 207
  DEL PEAK 14(9P23) WILD-TYPE  14  97
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED     29  207
  DEL PEAK 14(9P23) WILD-TYPE   14   97
     clus
vv    DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  NO                         29                          14
  YES                       207                          97
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, binary
                             cls
clus                            0   1
  DEL PEAK 14(9P23) MUTATED    95 142
  DEL PEAK 14(9P23) WILD-TYPE  36  75
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED     95  142
  DEL PEAK 14(9P23) WILD-TYPE   36   75
        clus
vv       DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  FEMALE                        95                          36
  MALE                         142                          75
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9P23) MUTATED       3                         1   220
  DEL PEAK 14(9P23) WILD-TYPE     2                         0   106
D36V13, multiclass
                           clus
vv                          DEL PEAK 14(9P23) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                           220
                           clus
vv                          DEL PEAK 14(9P23) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                             106
[1] 3 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 14(9P23) MUTATED     2 229
  DEL PEAK 14(9P23) WILD-TYPE   5 105
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(9P23) MUTATED      2  229
  DEL PEAK 14(9P23) WILD-TYPE    5  105
                        clus
vv                       DEL PEAK 14(9P23) MUTATED DEL PEAK 14(9P23) WILD-TYPE
  HISPANIC OR LATINO                             2                           5
  NOT HISPANIC OR LATINO                       229                         105
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 15(9P21.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(9P21.3) MUTATED   121 133
  DEL PEAK 15(9P21.3) WILD-TYPE  47  32
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          254                            79 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          133                            32 
$`DEL PEAK 15(9P21.3) MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
        3.02        16.47       111.09        32.42        70.16        28.08 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK 
       10.29        85.32        68.22        86.76        44.19         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       92.42        56.19        59.57        15.25        46.98        61.38 
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-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       29.23        93.21        54.31        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      110.24        47.87        13.68        17.72        23.11        29.72 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       10.22        15.19         4.18        38.93       124.47        87.62 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        5.56        24.07         4.01        21.93         5.72         9.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       14.60        48.79        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-A1IC 
        9.99        44.52        36.69        25.15         4.93         6.64 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
        7.00        17.56        13.15         0.20         0.13        23.15 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85         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        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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        55.69 
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-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
        6.18         9.53         2.73         7.96        14.56       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      111.91        56.02        25.08        26.99        60.49        53.16 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        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-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22         0.95        18.41        21.73        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       18.61        12.95         5.72        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-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
       17.72        11.80         1.87         1.51        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        9.04        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YW 
       15.72         6.71         3.58         5.36         2.20        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        11.01        23.80        14.24         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-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        12.92        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-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-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.99         0.13         0.16         7.23         0.85        11.61 
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-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       14.50        14.50        14.50        15.81         0.43        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 
        5.79        18.05         0.33         0.69         8.98        60.03 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
        2.99        10.98        71.01        11.84         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       18.67        21.07        13.12         3.72         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT 
        5.36         1.08         1.94        12.07         6.18         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

$`DEL PEAK 15(9P21.3) WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
        6.97         6.97         8.52       110.79        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG 
       81.24         8.38        21.14        88.50        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A51F 
       36.16        64.44       114.67        46.32        82.29        54.74 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK 
       31.30        32.28        52.01        22.06       142.45       108.79 
TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IB 
       75.65        11.44        11.31        13.22        10.03        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A183 
       19.36        14.83        19.00         0.20         6.31        12.20 
TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29M TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ 
        5.13         9.90        39.62        49.22        36.30        19.43 
TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       16.01        34.98         2.70        47.51        29.46        44.25 
TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3J5 TCGA-EE-A3JD 
       63.42        21.60        52.67         5.56        21.60        27.35 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7UA 
       38.40        76.41        78.44        13.08         6.58        13.28 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU 
        4.70         3.29        15.52        12.89        52.08         8.68 
TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A266 
        5.23         2.27        17.33         9.90        44.28        10.13 
TCGA-GN-A267 TCGA-GN-A4U8 TCGA-W3-A824 TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-AAA0 
       16.24        11.84       164.19       185.16         5.49        19.96 
TCGA-YG-AA3P 
        4.70 

  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                         0.13                          0.20 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       125.65                        185.16 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       13.745                        19.960 
[1] "0.1 - 125.7 (13.7)" "0.2 - 185.2 (20.0)"
[1] "hr=" "1.6"
D37V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(9P21.3) MUTATED   124 134
  DEL PEAK 15(9P21.3) WILD-TYPE  49  32
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          258                            81 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                          134                            32 
$`DEL PEAK 15(9P21.3) MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       17.03        16.57       112.04       112.57        71.80        28.08 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK 
       43.43       103.10       168.00        86.76        62.07        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
      171.58        56.19        59.57        58.06        46.98        86.93 
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-A3MV TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       45.30       174.84       145.12        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      125.79       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       11.61        15.19        58.52        89.13       161.00       137.79 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17       151.53        54.67         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV 
       11.34        22.29        11.11         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        68.25        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64         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       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 
       25.87       195.02        17.92        46.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      268.73        16.96       204.66       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB 
       47.54       248.65       134.40       162.48       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB 
      172.18       127.20        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       148.08        31.40        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        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-A19T TCGA-ER-A19W TCGA-ER-A2NC 
      162.08        50.89        37.25         8.88       148.18        43.82 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       15.16         7.00        34.82       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        20.91         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-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
      101.26       133.55        11.41       148.80        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        77.82        50.14        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-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
        0.16         7.23         2.04        11.74       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       62.79        32.48        39.58        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.33         0.69        63.02       121.08         4.01        42.08 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      105.04        24.03        54.38         8.61        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       59.41        52.34         3.75        22.68        43.73         2.20 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       10.36        15.16        36.03        23.64        93.07        11.74 

$`DEL PEAK 15(9P21.3) WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       61.02        12.99        16.67       133.25        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG 
       95.74        65.49        23.77       115.53        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A51F 
       42.08        66.08       130.72        46.32       166.52        55.73 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GK 
       56.35        32.94       135.75        79.59       228.99       170.20 
TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A1JW TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I0 
       95.24        29.06         3.65        25.18        66.25        20.38 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 
       23.44        28.60        15.68        54.02         6.35        12.20 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29M TCGA-EE-A2A1 
        8.65        26.89        68.15        80.61        56.84       102.90 
TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2MC 
       36.82        89.33        54.74        44.88        28.83        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      103.27       103.20        96.23        43.23        71.21        53.26 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A1A1 TCGA-ER-A2NF 
       36.95        27.35        50.76        77.75        79.99        16.37 
TCGA-ER-A3ET TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZK 
       80.32        38.27        29.46        94.39        28.08        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A5DY TCGA-GF-A3OT 
       74.73        26.56        27.02        77.88        19.30         9.90 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 TCGA-W3-A824 TCGA-W3-AA1W 
      139.89        10.13        64.44        46.36       212.22       219.16 
TCGA-WE-A8K1 TCGA-WE-AAA0 TCGA-YG-AA3P 
       38.56        30.18        14.43 

  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                         0.16                          3.65 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       369.93                        228.99 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                        49.79                         53.26 
[1] "0.2 - 369.9 (49.8)" "3.6 - 229.0 (53.3)"
[1] "hr=" "1.2"
D37V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 15(9P21.3) MUTATED                   49             2
  DEL PEAK 15(9P21.3) WILD-TYPE                 12             3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 15(9P21.3) MUTATED                                          57
  DEL PEAK 15(9P21.3) WILD-TYPE                                        15
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 15(9P21.3) MUTATED                   157
  DEL PEAK 15(9P21.3) WILD-TYPE                  52
D37V4, multiclass
                                           clus
vv                                          DEL PEAK 15(9P21.3) MUTATED
  DISTANT METASTASIS                                                 49
  PRIMARY TUMOR                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          57
  REGIONAL LYMPH NODE                                               157
                                           clus
vv                                          DEL PEAK 15(9P21.3) WILD-TYPE
  DISTANT METASTASIS                                                   12
  PRIMARY TUMOR                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            15
  REGIONAL LYMPH NODE                                                  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                            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB
  DEL PEAK 15(9P21.3) MUTATED            11       5      21       13       18
  DEL PEAK 15(9P21.3) WILD-TYPE           1       2       7        4        9
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 15(9P21.3) MUTATED         16        11        13         9
  DEL PEAK 15(9P21.3) WILD-TYPE        6         3         6         3
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 15(9P21.3) MUTATED          29          8         27         42
  DEL PEAK 15(9P21.3) WILD-TYPE         6          7          5         16
                               vv
clus                            STAGE IV
  DEL PEAK 15(9P21.3) MUTATED         17
  DEL PEAK 15(9P21.3) WILD-TYPE        2
D37V5, multiclass
             clus
vv            DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  I OR II NOS                          11                             1
  STAGE 0                               5                             2
  STAGE I                              21                             7
  STAGE IA                             13                             4
  STAGE IB                             18                             9
  STAGE II                             16                             6
  STAGE IIA                            11                             3
  STAGE IIB                            13                             6
  STAGE IIC                             9                             3
  STAGE III                            29                             6
  STAGE IIIA                            8                             7
  STAGE IIIB                           27                             5
  STAGE IIIC                           42                            16
  STAGE IV                             17                             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 15(9P21.3) MUTATED      51 53 56 47
  DEL PEAK 15(9P21.3) WILD-TYPE    12 18 18 20
D37V6, multiclass
       clus
vv      DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  T0+T1                          51                            12
  T2                             53                            18
  T3                             56                            18
  T4                             47                            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(9P21.3) MUTATED   125  49  29  34
  DEL PEAK 15(9P21.3) WILD-TYPE  43  12   9  13
D37V7, multiclass
    clus
vv   DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  N0                         125                            43
  N1                          49                            12
  N2                          29                             9
  N3                          34                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B M1C
  DEL PEAK 15(9P21.3) MUTATED   230   3   2   4   9
  DEL PEAK 15(9P21.3) WILD-TYPE  76   1   1   0   0
D37V8, multiclass
     clus
vv    DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  M0                          230                            76
  M1                            3                             1
  M1A                           2                             1
  M1B                           4                             0
  M1C                           9                             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 15(9P21.3) MUTATED   95 65
  DEL PEAK 15(9P21.3) WILD-TYPE 34 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     95   65
  DEL PEAK 15(9P21.3) WILD-TYPE   34   22
     clus
vv    DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  NO                           95                            34
  YES                          65                            22
[1] 2 2
[1] FALSE
D37V10, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED    37 228
  DEL PEAK 15(9P21.3) WILD-TYPE   6  76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     37  228
  DEL PEAK 15(9P21.3) WILD-TYPE    6   76
     clus
vv    DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  NO                           37                             6
  YES                         228                            76
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P21.3) MUTATED   109 157
  DEL PEAK 15(9P21.3) WILD-TYPE  22  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED    109  157
  DEL PEAK 15(9P21.3) WILD-TYPE   22   60
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  FEMALE                         109                            22
  MALE                           157                            60
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P21.3) MUTATED       4                         1   247
  DEL PEAK 15(9P21.3) WILD-TYPE     1                         0    79
D37V13, multiclass
                           clus
vv                          DEL PEAK 15(9P21.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                             247
                           clus
vv                          DEL PEAK 15(9P21.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                79
[1] 3 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 15(9P21.3) MUTATED     3 256
  DEL PEAK 15(9P21.3) WILD-TYPE   4  78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      3  256
  DEL PEAK 15(9P21.3) WILD-TYPE    4   78
                        clus
vv                       DEL PEAK 15(9P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         256
                        clus
vv                       DEL PEAK 15(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            78
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 16(10P15.3) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(10P15.3) MUTATED   85 98
  DEL PEAK 16(10P15.3) WILD-TYPE 83 67
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           183                            150 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                            98                             67 
$`DEL PEAK 16(10P15.3) MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        6.97         6.97        16.47       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      110.79        28.08        10.29        88.50        86.76        11.41 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
        7.50         6.31        56.19        64.44        59.57        46.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       13.32        24.00         9.34        26.37        29.23        54.74 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       54.31        32.28        25.78        52.01        47.87        13.68 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP 
       23.11        22.06        10.22         4.18       142.45        87.62 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
        5.56        24.07        21.93         5.72         9.90        11.31 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       14.60        35.80        51.12        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A44R 
       44.52        36.69        25.15         4.93        17.56         0.20 
TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 
       19.00         6.31         8.12         1.12         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       60.23         9.21         1.18         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       39.62         9.50        12.03         8.09         9.99        30.44 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GE 
       32.15         8.09        36.30         9.67        51.12        60.00 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       47.21        30.08        19.43        28.31        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        5.42         1.15        13.02        98.27         2.70         6.18 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS 
       44.25         7.96        14.56       125.65        56.02        53.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH 
        5.56       124.31       122.73         3.68        30.15        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19D 
        0.95        18.41        21.73        33.60         5.72         3.52 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S 
       11.90       114.15        34.88        13.45        34.68        36.07 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
       17.72        11.80         1.87         1.51        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 
       15.72         6.71         3.58         3.29         3.45        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
        7.17        30.87        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-GN-A8LK 
       10.13        16.24        15.42        12.16        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 
       14.50        14.50        15.81        11.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZM 
      164.19         8.98        10.98        71.01        11.84        18.67 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        3.72        21.83         5.36         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         6.67         5.98 

$`DEL PEAK 16(10P15.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
        3.02         8.52        22.55        45.83        81.24        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
        8.38        21.14        68.22        44.19        36.16        92.42 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML 
      114.67        15.25        46.32        82.29        61.38         6.31 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL 
      103.59        93.21        31.30        21.44        32.61       110.24 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       17.72        29.72        15.19       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I0 
      124.47        11.44         4.01        13.22        48.79        10.03 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13        23.15        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A 
       10.55         1.35        12.20         4.34        15.85         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A29V 
        9.90        37.97        11.15        62.79         8.84         2.43 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GK 
       11.31        49.22        36.33        34.29        17.98        16.01 
TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       35.54        34.98        36.33         8.84        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       29.46         2.73        63.42       111.91        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
       21.60        60.49        52.67        51.62        13.81        15.95 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        31.40        18.61        12.95        38.40        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       25.18         3.78        11.11         4.21        28.60        42.84 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-FR-A44A TCGA-FR-A7U9 
        9.57         6.58        78.44        13.08        85.74         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 
       13.28         2.20         4.70        64.47        11.01        15.52 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS 
        3.39        19.53        12.92        12.89        52.08        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 
       40.64         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-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
        0.16        17.33         9.90         0.85        11.61        44.28 
TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       84.72        14.70        11.84         0.43         5.79        18.05 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       60.03         2.99       185.16         5.49         6.48         7.10 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-A8RT 
       21.07        13.12         3.42         1.08        19.96         8.22 

  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                          0.20                           0.13 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                        164.19                         185.16 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                        14.500                         15.685 
[1] "0.2 - 164.2 (14.5)" "0.1 - 185.2 (15.7)"
[1] "hr=" "1.3"
D38V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(10P15.3) MUTATED   86 98
  DEL PEAK 16(10P15.3) WILD-TYPE 87 68
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                           184                            155 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                            98                             68 
$`DEL PEAK 16(10P15.3) MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       61.02        12.99        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      133.25        28.08        43.43       115.53        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
      113.52        12.10        56.19        66.08        59.57        46.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       60.23        24.53         9.34        39.75        45.30        55.73 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
      145.12        32.94        26.89       135.75       137.92       178.32 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP 
      125.19        79.59        11.61        58.52       228.99       137.79 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      129.63       117.17        18.12        22.29        11.11         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       25.18        22.95        36.03       117.21       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 
       35.93       107.34        61.18        53.92        65.92       215.44 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 
       10.16        54.02         8.65        94.98        33.73        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H 
        4.96       133.81       168.26        13.55        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        2.60        56.84        18.61        56.42        37.35        55.92 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
      369.93       195.02        17.92        36.82        39.29        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN 
      161.03       208.04        48.72        89.33        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
      126.81        13.91        14.30        55.59       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
       19.76       103.20        16.96       204.66       158.63       167.90 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        53.26       124.31       122.73         3.68        54.51 
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-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
       53.19       201.80        51.35       109.58       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX 
       92.98        15.72       210.08        15.16        94.39        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        20.91         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       15.45         9.70        32.75       101.26       133.55        11.41 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GF-A4EO 
       26.56        49.48        27.09        66.67        28.73         7.23 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 
      117.93        10.13        64.44        62.79        32.48        12.62 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 
       50.10        21.37        59.41        65.88       294.77         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ 
        0.69       212.22        63.02        42.08       105.04        24.03 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 
       90.28        52.34        22.68        43.73        10.36        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        93.07        11.74 

$`DEL PEAK 16(10P15.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       17.03        16.67        31.59        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
       65.49        23.77       168.00        62.07        42.08       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML 
      130.72        58.06        46.32       166.52        86.93        13.87 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL 
      103.59       174.84        56.35        22.62        63.81       125.79 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       18.18        30.84        15.19       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      161.00        29.06       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC 
       11.34        66.25        48.89        20.38        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       28.60        10.49        15.68        13.87        17.85        68.25 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.29        52.01         6.35        12.20        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B 
       14.70        26.89       151.27        91.56        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A0 
       47.84        13.97        63.78        14.47        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL 
      102.90        86.14        67.43       314.56        54.74        79.66 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       44.88        94.82        21.67        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      268.73        96.23       203.05        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JD 
      134.40        71.21        51.62        13.81        23.47        27.35 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        35.44        13.94        50.76        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       48.89        26.37         6.44        61.05        44.05        50.89 
TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A7UA 
        8.88        79.99        16.37       174.21         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB 
       34.82        29.46       216.92       228.59        28.08        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT 
       40.27        47.38        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-A4FB 
       27.02        77.82        50.14       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-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 
       19.30         9.90         2.04        11.74       139.89        84.72 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A828 
       39.58        46.36       357.04         6.67        18.05       121.08 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
        4.01       219.16        38.56        54.38         8.61        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-A8RT 
       59.41         3.75         2.20        30.18        23.64 

  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                          0.33                           0.16 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                        369.93                         357.04 
  DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE 
                        54.265                         47.540 
[1] "0.3 - 369.9 (54.3)" "0.2 - 357.0 (47.5)"
[1] "hr=" "1.1"
D38V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 16(10P15.3) MUTATED                   35             2
  DEL PEAK 16(10P15.3) WILD-TYPE                 26             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 16(10P15.3) MUTATED                                          47
  DEL PEAK 16(10P15.3) WILD-TYPE                                        25
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 16(10P15.3) MUTATED                   107
  DEL PEAK 16(10P15.3) WILD-TYPE                 102
D38V4, multiclass
                                           clus
vv                                          DEL PEAK 16(10P15.3) MUTATED
  DISTANT METASTASIS                                                  35
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           47
  REGIONAL LYMPH NODE                                                107
                                           clus
vv                                          DEL PEAK 16(10P15.3) WILD-TYPE
  DISTANT METASTASIS                                                    26
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             25
  REGIONAL LYMPH NODE                                                  102
[1] 4 2
[1] 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(10P15.3) MUTATED             8       4      14       11       16
  DEL PEAK 16(10P15.3) WILD-TYPE           4       3      14        6       11
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 16(10P15.3) MUTATED         13         7         7         5
  DEL PEAK 16(10P15.3) WILD-TYPE        9         7        12         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 16(10P15.3) MUTATED          21         11         16         35
  DEL PEAK 16(10P15.3) WILD-TYPE        14          4         16         23
                                vv
clus                             STAGE IV
  DEL PEAK 16(10P15.3) MUTATED          8
  DEL PEAK 16(10P15.3) WILD-TYPE       11
D38V5, multiclass
             clus
vv            DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  I OR II NOS                            8                              4
  STAGE 0                                4                              3
  STAGE I                               14                             14
  STAGE IA                              11                              6
  STAGE IB                              16                             11
  STAGE II                              13                              9
  STAGE IIA                              7                              7
  STAGE IIB                              7                             12
  STAGE IIC                              5                              7
  STAGE III                             21                             14
  STAGE IIIA                            11                              4
  STAGE IIIB                            16                             16
  STAGE IIIC                            35                             23
  STAGE IV                               8                             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 16(10P15.3) MUTATED      37 41 31 44
  DEL PEAK 16(10P15.3) WILD-TYPE    26 30 43 23
D38V6, multiclass
       clus
vv      DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  T0+T1                           37                             26
  T2                              41                             30
  T3                              31                             43
  T4                              44                             23
[1] 4 2
[1] 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(10P15.3) MUTATED   92 36 21 24
  DEL PEAK 16(10P15.3) WILD-TYPE 76 25 17 23
D38V7, multiclass
    clus
vv   DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  N0                           92                             76
  N1                           36                             25
  N2                           21                             17
  N3                           24                             23
[1] 4 2
[1] 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(10P15.3) MUTATED   171   1   1   1   5
  DEL PEAK 16(10P15.3) WILD-TYPE 135   3   2   3   4
D38V8, multiclass
     clus
vv    DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  M0                           171                            135
  M1                             1                              3
  M1A                            1                              2
  M1B                            1                              3
  M1C                            5                              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"
D38V9, binary
                                cls
clus                              0  1
  DEL PEAK 16(10P15.3) MUTATED   67 50
  DEL PEAK 16(10P15.3) WILD-TYPE 62 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED     67   50
  DEL PEAK 16(10P15.3) WILD-TYPE   62   37
     clus
vv    DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  NO                            67                             62
  YES                           50                             37
[1] 2 2
[1] FALSE
D38V10, binary
                                cls
clus                               0   1
  DEL PEAK 16(10P15.3) MUTATED    22 168
  DEL PEAK 16(10P15.3) WILD-TYPE  21 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED     22  168
  DEL PEAK 16(10P15.3) WILD-TYPE   21  136
     clus
vv    DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  NO                            22                             21
  YES                          168                            136
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, binary
                                cls
clus                               0   1
  DEL PEAK 16(10P15.3) MUTATED    78 113
  DEL PEAK 16(10P15.3) WILD-TYPE  53 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED     78  113
  DEL PEAK 16(10P15.3) WILD-TYPE   53  104
        clus
vv       DEL PEAK 16(10P15.3) MUTATED DEL PEAK 16(10P15.3) WILD-TYPE
  FEMALE                           78                             53
  MALE                            113                            104
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10P15.3) MUTATED       1                         0   179
  DEL PEAK 16(10P15.3) WILD-TYPE     4                         1   147
D38V13, multiclass
                           clus
vv                          DEL PEAK 16(10P15.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              179
                           clus
vv                          DEL PEAK 16(10P15.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                147
[1] 3 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 16(10P15.3) MUTATED     4 183
  DEL PEAK 16(10P15.3) WILD-TYPE   3 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10P15.3) MUTATED      4  183
  DEL PEAK 16(10P15.3) WILD-TYPE    3  151
                        clus
vv                       DEL PEAK 16(10P15.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          183
                        clus
vv                       DEL PEAK 16(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            151
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 17(10Q21.1) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(10Q21.1) MUTATED    98 100
  DEL PEAK 17(10Q21.1) WILD-TYPE  70  65
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           198                            135 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           100                             65 
$`DEL PEAK 17(10Q21.1) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        6.97       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        86.76        11.41         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CE 
       92.42        56.19        64.44        59.57        15.25        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        29.23        54.74 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       54.31        32.28        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM 
       17.72        23.11        22.06        10.22         4.18        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      124.47        87.62        24.07        21.93         5.72         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.31        13.22        14.60        35.80        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-A5UL TCGA-EB-A5UN TCGA-EE-A17Z 
       14.83         0.20        19.00        13.35        13.22         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I 
        8.12         1.12         4.31        60.23         9.21         1.18 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       11.15         8.55        36.85         1.08        39.62        12.03 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.09        30.44        32.15         8.09        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        1.15        13.02        36.33        98.27         2.70         6.18 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM 
        9.53         2.73        44.25         7.96       125.65        56.02 
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-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-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22         0.95        18.41        21.73        33.60        31.40 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L 
        5.72         3.78         3.52        11.90        34.88        13.45 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE 
       34.68        36.07         6.58        17.72        11.80         1.51 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       12.62        11.74        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX 
       85.74        15.72         6.71         3.58         3.29         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       11.01        23.80        14.24         7.33         7.30        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        8.22        11.08        30.87        12.92        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.81         8.68        27.39         0.82         7.36        28.73 
TCGA-FS-A4FB TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
        5.98         0.16         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
       31.33        10.13        16.24        15.42        12.16        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 
       10.65        14.50        14.50        15.81        11.05         0.33 
TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
        0.69         8.98        71.01        11.84         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       18.67         3.72         3.42        21.83         5.36         1.08 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         6.18         4.70         6.67         5.98 

$`DEL PEAK 17(10Q21.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB 
        3.02         6.97        16.47         8.52        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF 
       10.29        85.32         8.38        21.14        68.22        44.19 
TCGA-D3-A2JH TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       36.16       114.67        46.98        46.32        82.29        61.38 
TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL 
        6.31        93.21        31.30        21.44        32.61       110.24 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ 
       29.72        15.19       142.45       108.79        38.93        11.44 
TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB 
        5.56         4.01        48.79        51.12        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        23.15 
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-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        4.34        15.85         7.99         9.90        37.97        62.79 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.50         8.84         9.99         2.43        11.31        49.22 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME 
       16.01        35.54        34.98         8.84        47.51        29.46 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       14.56        63.42       111.91        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JD 
       60.49        53.16        52.67        51.62        15.95        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-A1A1 
      114.15         4.21        28.60        42.84         9.57        78.44 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FR-A7UA 
        1.87        13.08         9.04         6.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE 
        2.20         4.70        64.47        15.52         3.39        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-FS-A4FD 
       53.85         3.22        14.20        10.78         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 
        0.20         0.99         0.13        17.33         9.90        84.72 
TCGA-GN-A26D TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 
       14.70        14.50         0.43         5.79        18.05       164.19 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN 
       60.03         2.99        10.98       185.16         5.49        21.07 
TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-Z2-A8RT 
       13.12        19.96         8.22 

  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                          0.16                           0.13 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                        125.65                         185.16 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                        14.025                         15.950 
[1] "0.2 - 125.7 (14.0)" "0.1 - 185.2 (15.9)"
[1] "hr=" "1.2"
D39V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(10Q21.1) MUTATED   101 100
  DEL PEAK 17(10Q21.1) WILD-TYPE  72  66
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           201                            138 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                           100                             66 
$`DEL PEAK 17(10Q21.1) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       12.99       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        86.76        11.87       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CE 
      171.58        56.19        66.08        59.57        58.06        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        45.30        55.73 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
      145.12        32.94        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM 
       18.18       125.19        79.59        11.61        58.52        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 
      161.00       137.79       117.17       151.53        54.67        18.12 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       22.29        11.11         9.90        25.18        66.25        22.95 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       36.03       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH 
       53.92        65.92       215.44        15.68        10.16        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 
       17.29        52.01         8.65        94.98        33.73         4.96 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
      133.81       168.26        13.55        13.97        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
        2.60        56.84        56.42        37.35       369.93       195.02 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       17.92        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
      314.56       161.03       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       126.81        13.91        14.30        55.59        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG 
      129.27        28.83        19.76        47.28       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       16.96       158.63       167.90        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
      109.58       148.08        31.40         9.17        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T 
       13.02       152.35       131.51       162.08        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV 
      148.18        43.82        20.15        31.27        32.05        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.16        94.39        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.79        27.72       357.37        53.52        15.45        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38       101.26       133.55        11.41        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3TV TCGA-GF-A4EO 
       27.09        66.67        28.73        26.73         0.16         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        2.04        11.74       139.89       117.93        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       62.79        32.48        46.36        12.62        50.10        59.41 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 
       65.88       294.77         0.33         0.69        63.02       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       24.03        54.38         8.61        90.28        52.34         3.75 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       22.68        43.73         2.20        10.36        15.16        36.03 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        93.07        11.74 

$`DEL PEAK 17(10Q21.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB 
       17.03        61.02        16.57        16.67        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF 
       43.43       103.10        65.49        23.77       168.00        62.07 
TCGA-D3-A2JH TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       42.08       130.72        46.98        46.32       166.52        86.93 
TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL 
       13.87       174.84        56.35        22.62        63.81       125.79 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ 
       30.84        15.19       228.99       170.20        89.13        29.06 
TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY 
      129.63         3.65         6.41        11.34        48.89       117.21 
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        68.25         6.35        12.20        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A 
       14.70        26.89        68.15       151.27        91.56        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       80.61        47.84        63.78        18.61        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT 
       25.87        46.82       102.90        54.74        79.66        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-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       134.40       162.48        71.21 
TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JD TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.62        23.47        27.35        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M 
       77.75        98.40        26.37       268.93         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES 
       44.05        50.89        79.99        23.34        16.37       247.04 
TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
       80.32         7.00        38.27        34.82        29.46       216.92 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
       28.08        48.85        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-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-A5DY TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A8LL TCGA-LH-A9QB 
       19.30         9.90        84.72        39.58        21.37       357.04 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        6.67        18.05       212.22       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-Z2-A8RT 
      219.16        38.56        56.98        59.41        30.18        23.64 

  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                          0.16                           0.20 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                        369.93                         357.04 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                         53.26                          47.69 
[1] "0.2 - 369.9 (53.3)" "0.2 - 357.0 (47.7)"
[1] "hr=" "1"  
D39V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 17(10Q21.1) MUTATED                   33             4
  DEL PEAK 17(10Q21.1) WILD-TYPE                 28             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 17(10Q21.1) MUTATED                                          51
  DEL PEAK 17(10Q21.1) WILD-TYPE                                        21
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 17(10Q21.1) MUTATED                   120
  DEL PEAK 17(10Q21.1) WILD-TYPE                  89
D39V4, multiclass
                                           clus
vv                                          DEL PEAK 17(10Q21.1) MUTATED
  DISTANT METASTASIS                                                  33
  PRIMARY TUMOR                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           51
  REGIONAL LYMPH NODE                                                120
                                           clus
vv                                          DEL PEAK 17(10Q21.1) WILD-TYPE
  DISTANT METASTASIS                                                    28
  PRIMARY TUMOR                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             21
  REGIONAL LYMPH NODE                                                   89
[1] 4 2
[1] 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(10Q21.1) MUTATED             9       3      16       13       16
  DEL PEAK 17(10Q21.1) WILD-TYPE           3       4      12        4       11
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 17(10Q21.1) MUTATED         12         6        10         5
  DEL PEAK 17(10Q21.1) WILD-TYPE       10         8         9         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 17(10Q21.1) MUTATED          24         11         20         34
  DEL PEAK 17(10Q21.1) WILD-TYPE        11          4         12         24
                                vv
clus                             STAGE IV
  DEL PEAK 17(10Q21.1) MUTATED         12
  DEL PEAK 17(10Q21.1) WILD-TYPE        7
D39V5, multiclass
             clus
vv            DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  I OR II NOS                            9                              3
  STAGE 0                                3                              4
  STAGE I                               16                             12
  STAGE IA                              13                              4
  STAGE IB                              16                             11
  STAGE II                              12                             10
  STAGE IIA                              6                              8
  STAGE IIB                             10                              9
  STAGE IIC                              5                              7
  STAGE III                             24                             11
  STAGE IIIA                            11                              4
  STAGE IIIB                            20                             12
  STAGE IIIC                            34                             24
  STAGE IV                              12                              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 17(10Q21.1) MUTATED      40 45 35 45
  DEL PEAK 17(10Q21.1) WILD-TYPE    23 26 39 22
D39V6, multiclass
       clus
vv      DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  T0+T1                           40                             23
  T2                              45                             26
  T3                              35                             39
  T4                              45                             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                             N0 N1 N2 N3
  DEL PEAK 17(10Q21.1) MUTATED   95 43 23 26
  DEL PEAK 17(10Q21.1) WILD-TYPE 73 18 15 21
D39V7, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  N0                           95                             73
  N1                           43                             18
  N2                           23                             15
  N3                           26                             21
[1] 4 2
[1] 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(10Q21.1) MUTATED   181   1   2   3   7
  DEL PEAK 17(10Q21.1) WILD-TYPE 125   3   1   1   2
D39V8, multiclass
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  M0                           181                            125
  M1                             1                              3
  M1A                            2                              1
  M1B                            3                              1
  M1C                            7                              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"
D39V9, binary
                                cls
clus                              0  1
  DEL PEAK 17(10Q21.1) MUTATED   76 54
  DEL PEAK 17(10Q21.1) WILD-TYPE 53 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     76   54
  DEL PEAK 17(10Q21.1) WILD-TYPE   53   33
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  NO                            76                             53
  YES                           54                             33
[1] 2 2
[1] FALSE
D39V10, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED    25 182
  DEL PEAK 17(10Q21.1) WILD-TYPE  18 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     25  182
  DEL PEAK 17(10Q21.1) WILD-TYPE   18  122
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  NO                            25                             18
  YES                          182                            122
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED    87 121
  DEL PEAK 17(10Q21.1) WILD-TYPE  44  96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     87  121
  DEL PEAK 17(10Q21.1) WILD-TYPE   44   96
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  FEMALE                           87                             44
  MALE                            121                             96
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(10Q21.1) MUTATED       1                         0   194
  DEL PEAK 17(10Q21.1) WILD-TYPE     4                         1   132
D39V13, multiclass
                           clus
vv                          DEL PEAK 17(10Q21.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              194
                           clus
vv                          DEL PEAK 17(10Q21.1) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                132
[1] 3 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 17(10Q21.1) MUTATED     4 200
  DEL PEAK 17(10Q21.1) WILD-TYPE   3 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED      4  200
  DEL PEAK 17(10Q21.1) WILD-TYPE    3  134
                        clus
vv                       DEL PEAK 17(10Q21.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          200
                        clus
vv                       DEL PEAK 17(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            134
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 18(10Q23.31) MUTATION ANALYSIS
D40V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 18(10Q23.31) MUTATED   105 103
  DEL PEAK 18(10Q23.31) WILD-TYPE  63  62
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            208                             125 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            103                              62 
$`DEL PEAK 18(10Q23.31) MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        6.97         6.97        16.47       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      110.79        28.08        22.55        88.50        86.76        11.41 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        7.50         6.31        92.42        56.19        64.44        59.57 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       15.25        46.98        61.38        13.32        24.00         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
      103.59        26.37        29.23        54.74        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM 
       23.11        29.72        22.06        10.22         4.18        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      124.47        87.62        24.07        21.93         5.72         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.31        13.22        14.60        35.80        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-A5UL TCGA-EB-A5UN TCGA-EE-A17Y 
       14.83         0.20        19.00        13.35        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        60.23        15.85 
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        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       39.62        12.03         8.09        30.44        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       17.98        60.00        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        55.69         5.42         1.15        13.02        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG 
       98.27         2.70         6.18         9.53         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU 
        7.96        14.56       125.65        56.02        26.99         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 
        0.95        18.41        21.73        33.60        31.40         5.72 
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-A19T TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
       36.07         6.58        11.80         1.51        12.62        11.74 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        6.71         3.58         3.29        11.01        23.80        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.33         7.30        20.38         8.22        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-FW-A3I3 TCGA-FW-A3TU 
        0.82         7.36        28.73         5.98         0.20         0.13 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        0.16         7.23         0.85        44.28        31.33        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       16.24        12.16        11.84        10.65        14.50        14.50 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       15.81        11.05         0.33         0.69       164.19         8.98 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       71.01        11.84         6.48         7.10        18.67         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.42        21.83         5.36         1.08         1.94        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         4.70         6.67         5.98 

$`DEL PEAK 18(10Q23.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
        3.02         8.52        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3BZ 
        8.38        21.14        68.22        44.19        36.16       114.67 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51R 
       46.32        82.29         6.31        93.21        31.30        32.61 
TCGA-D3-A5GL TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ 
      110.24        15.19       142.45       108.79        38.93        11.44 
TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB 
        5.56         4.01        48.79        51.12        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        23.15 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C 
        0.20        11.57         1.35        12.20         5.13         4.34 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R 
        7.99         9.90        37.97        62.79         9.50         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT 
        9.99         2.43        49.22        16.01        35.54        34.98 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
        8.84        47.51        29.46        63.42       111.91        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J7 
       21.60        60.49        53.16        52.67        51.62        21.60 
TCGA-EE-A3JD TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       27.35        18.61        12.95        38.40        76.41        25.18 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       11.11       114.15         4.21        28.60        42.84         9.57 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       17.72        78.44         1.87        13.08         9.04         6.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX 
        5.36        13.28         2.20         4.70        64.47         3.45 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
       15.52         3.39        19.53         7.17        12.89        52.08 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
       49.15        40.64         5.23        53.85         3.22        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT 
       10.78         6.41         2.27         0.99        17.33         9.90 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LL TCGA-LH-A9QB 
       11.61        84.72        15.42        14.70        14.50         0.43 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
        5.79        18.05        60.03         2.99        10.98       185.16 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-Z2-A8RT 
        5.49        21.07        13.12        19.96         8.22 

  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                           0.13                            0.13 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                         164.19                          185.16 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                          14.50                           15.52 
[1] "0.1 - 164.2 (14.5)" "0.1 - 185.2 (15.5)"
[1] "hr=" "1.1"
D40V2, survival
                                 sevent
clus2                               0   1
  DEL PEAK 18(10Q23.31) MUTATED   108 104
  DEL PEAK 18(10Q23.31) WILD-TYPE  65  62
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            212                             127 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                            104                              62 
$`DEL PEAK 18(10Q23.31) MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       61.02        12.99        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      133.25        28.08        31.59       115.53        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        12.10       171.58        56.19        66.08        59.57 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06        46.98        86.93        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
      103.59        39.75        45.30        55.73       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        26.89       135.75       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM 
      125.19        30.84        79.59        11.61        58.52        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX 
      161.00       137.79       117.17       151.53        54.67         6.41 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       18.12        22.29        11.11         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 
       54.02        17.29        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       133.81        91.56       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        64.64         2.60        56.84        56.42 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
       37.35       369.93       195.02        17.92        46.82        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        47.28       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      158.63       167.90       248.65        53.26       124.31       122.73 
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-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
      127.20        36.95        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
      109.58       148.08        31.40         9.17        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T 
       13.02       152.35       131.51       162.08        37.25         8.88 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL 
       43.82        20.15        31.27        32.05        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       210.08        15.16 
TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       94.39       228.59       202.65        20.91         7.79        27.72 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      357.37        53.52        15.45        32.75        47.38       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 
      133.55        11.41        26.56        49.48        27.09        66.67 
TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO 
       28.73        26.73         0.20        47.54         0.16         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        2.04       139.89       117.93        10.13        64.44        32.48 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X 
       46.36        12.62        50.10        59.41        65.88       294.77 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ 
        0.33         0.69       212.22        63.02       105.04        24.03 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       54.38         8.61        90.28        52.34         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
       43.73         2.20        10.36        15.16        36.03        14.43 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

$`DEL PEAK 18(10Q23.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       17.03        16.67        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3BZ 
       65.49        23.77       168.00        62.07        42.08       130.72 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51R 
       46.32       166.52        13.87       174.84        56.35        63.81 
TCGA-D3-A5GL TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ 
      125.79        15.19       228.99       170.20        89.13        29.06 
TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
      129.63         3.65        11.34        48.89       117.21        20.38 
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-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 
       68.25         6.35        12.20        29.82        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       68.15       151.27        63.35        80.61        47.84        63.78 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GK 
       18.61        14.47        55.92        25.87       102.90        54.74 
TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MJ 
       79.66        44.88        21.67        61.51       103.27        96.23 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      203.05        47.54        43.23       134.40       162.48        71.21 
TCGA-EE-A3AC TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.62        64.08        27.35        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M 
       77.75        98.40        26.37       268.93         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF 
       44.05        50.89       148.18        79.99        23.34        16.37 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      247.04        80.32         7.00        38.27        34.82        29.46 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
      216.92        48.59        28.08        48.85        40.27         9.70 
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-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       50.14       174.84        12.43        49.45        77.88        22.92 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
       19.30         9.90        11.74        84.72        62.79        39.58 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1O 
       21.37       357.04         6.67        18.05       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 
       42.08       219.16        38.56        56.98        59.41        30.18 
TCGA-Z2-A8RT 
       23.64 

  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                           0.16                            3.65 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                         369.93                          357.04 
  DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE 
                         52.175                          48.890 
[1] "0.2 - 369.9 (52.2)" "3.6 - 357.0 (48.9)"
[1] "hr=" "1.1"
D40V3, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 18(10Q23.31) MUTATED                   36             4
  DEL PEAK 18(10Q23.31) WILD-TYPE                 25             1
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 18(10Q23.31) MUTATED                                          51
  DEL PEAK 18(10Q23.31) WILD-TYPE                                        21
                                 vv
clus                              REGIONAL LYMPH NODE
  DEL PEAK 18(10Q23.31) MUTATED                   128
  DEL PEAK 18(10Q23.31) WILD-TYPE                  81
D40V4, multiclass
                                           clus
vv                                          DEL PEAK 18(10Q23.31) MUTATED
  DISTANT METASTASIS                                                   36
  PRIMARY TUMOR                                                         4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            51
  REGIONAL LYMPH NODE                                                 128
                                           clus
vv                                          DEL PEAK 18(10Q23.31) WILD-TYPE
  DISTANT METASTASIS                                                     25
  PRIMARY TUMOR                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                              21
  REGIONAL LYMPH NODE                                                    81
[1] 4 2
[1] 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(10Q23.31) MUTATED             8       3      17       13       16
  DEL PEAK 18(10Q23.31) WILD-TYPE           4       4      11        4       11
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 18(10Q23.31) MUTATED         12         8        10         6
  DEL PEAK 18(10Q23.31) WILD-TYPE       10         6         9         6
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 18(10Q23.31) MUTATED          26         11         21         35
  DEL PEAK 18(10Q23.31) WILD-TYPE         9          4         11         23
                                 vv
clus                              STAGE IV
  DEL PEAK 18(10Q23.31) MUTATED         15
  DEL PEAK 18(10Q23.31) WILD-TYPE        4
D40V5, multiclass
             clus
vv            DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  I OR II NOS                             8                               4
  STAGE 0                                 3                               4
  STAGE I                                17                              11
  STAGE IA                               13                               4
  STAGE IB                               16                              11
  STAGE II                               12                              10
  STAGE IIA                               8                               6
  STAGE IIB                              10                               9
  STAGE IIC                               6                               6
  STAGE III                              26                               9
  STAGE IIIA                             11                               4
  STAGE IIIB                             21                              11
  STAGE IIIC                             35                              23
  STAGE IV                               15                               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 18(10Q23.31) MUTATED      45 46 38 47
  DEL PEAK 18(10Q23.31) WILD-TYPE    18 25 36 20
D40V6, multiclass
       clus
vv      DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  T0+T1                            45                              18
  T2                               46                              25
  T3                               38                              36
  T4                               47                              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 18(10Q23.31) MUTATED   98 46 24 28
  DEL PEAK 18(10Q23.31) WILD-TYPE 70 15 14 19
D40V7, multiclass
    clus
vv   DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  N0                            98                              70
  N1                            46                              15
  N2                            24                              14
  N3                            28                              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
  DEL PEAK 18(10Q23.31) MUTATED   190   2   2   3   9
  DEL PEAK 18(10Q23.31) WILD-TYPE 116   2   1   1   0
D40V8, multiclass
     clus
vv    DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  M0                            190                             116
  M1                              2                               2
  M1A                             2                               1
  M1B                             3                               1
  M1C                             9                               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 18(10Q23.31) MUTATED   77 56
  DEL PEAK 18(10Q23.31) WILD-TYPE 52 31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     77   56
  DEL PEAK 18(10Q23.31) WILD-TYPE   52   31
     clus
vv    DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  NO                             77                              52
  YES                            56                              31
[1] 2 2
[1] FALSE
D40V10, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED    28 190
  DEL PEAK 18(10Q23.31) WILD-TYPE  15 114
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     28  190
  DEL PEAK 18(10Q23.31) WILD-TYPE   15  114
     clus
vv    DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  NO                             28                              15
  YES                           190                             114
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED    92 127
  DEL PEAK 18(10Q23.31) WILD-TYPE  39  90
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED     92  127
  DEL PEAK 18(10Q23.31) WILD-TYPE   39   90
        clus
vv       DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
  FEMALE                            92                              39
  MALE                             127                              90
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10Q23.31) MUTATED       2                         0   204
  DEL PEAK 18(10Q23.31) WILD-TYPE     3                         1   122
D40V13, multiclass
                           clus
vv                          DEL PEAK 18(10Q23.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               204
                           clus
vv                          DEL PEAK 18(10Q23.31) WILD-TYPE
  ASIAN                                                   3
  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"
D40V14, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10Q23.31) MUTATED     4 210
  DEL PEAK 18(10Q23.31) WILD-TYPE   3 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10Q23.31) MUTATED      4  210
  DEL PEAK 18(10Q23.31) WILD-TYPE    3  124
                        clus
vv                       DEL PEAK 18(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           210
                        clus
vv                       DEL PEAK 18(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             124
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 19(10Q26.3) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(10Q26.3) MUTATED   109 105
  DEL PEAK 19(10Q26.3) WILD-TYPE  59  60
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           214                            119 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           105                             60 
$`DEL PEAK 19(10Q26.3) MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        6.97         6.97        16.47       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      110.79        28.08        22.55        88.50        86.76        11.41 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
        7.50         6.31        92.42        56.19        59.57        15.25 
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 
       29.23        54.74        54.31        32.28        21.44        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       52.01        47.87        13.68        17.72        23.11        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN 
       22.06        10.22         4.18       142.45        75.65       124.47 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       87.62        24.07        21.93         5.72         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-A5UL TCGA-EB-A5UN TCGA-EE-A17Z 
       14.83         0.20        19.00        13.35        13.22         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        8.12         1.12         4.31        60.23        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
        1.18        11.15         8.55        36.85        39.62        12.03 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
        8.09        30.44        32.15         8.09        11.31        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       47.21        30.08        19.43        28.31        33.83        55.69 
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-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        2.70         6.18         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU 
        7.96        14.56       125.65        56.02        26.99         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73         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-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22         0.95        18.41        21.73        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       18.61         5.72        25.18         3.78         3.52        11.90 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       34.88        13.45        34.68        36.07         6.58        17.72 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET 
       11.80         1.51        13.08        12.62        11.74         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        6.71         3.58         3.29         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        17.33         7.23         0.85        44.28        31.33 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       10.13        12.16        11.84        10.65        14.50        14.50 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       15.81        11.05         0.33         0.69       164.19         8.98 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       71.01        11.84         6.48         7.10        18.67         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.42        21.83         5.36         1.08         1.94        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         4.70         6.67         5.98 

$`DEL PEAK 19(10Q26.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
        3.02         8.52        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JO 
        8.38        21.14        68.22        44.19        36.16        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A51E 
      114.67        46.98        46.32        82.29         6.31        93.21 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL 
       31.30        32.61       110.24        15.19       108.79        38.93 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1IB 
       11.44         5.56         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        23.15 
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        62.79         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        60.49        53.16        52.67        51.62        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-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z4 
        5.36        13.28         2.20         4.70        64.47        15.52 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
        3.39         8.22        19.53         7.17        12.89        52.08 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
       49.15        40.64         5.23        53.85         3.22        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GF-A3OT TCGA-GF-A6C9 
       10.78         6.41         0.20         0.99         9.90        11.61 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LL TCGA-LH-A9QB 
       84.72        16.24        15.42        14.70        14.50         0.43 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
        5.79        18.05        60.03         2.99        10.98       185.16 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-Z2-A8RT 
        5.49        21.07        13.12        19.96         8.22 

  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                        164.19                         185.16 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                         14.58                          15.19 
[1] "0.1 - 164.2 (14.6)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.1"
D41V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(10Q26.3) MUTATED   112 105
  DEL PEAK 19(10Q26.3) WILD-TYPE  61  61
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           217                            122 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                           105                             61 
$`DEL PEAK 19(10Q26.3) MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       61.02        12.99        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      133.25        28.08        31.59       115.53        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
      113.52        12.10       171.58        56.19        59.57        58.06 
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 
       45.30        55.73       145.12        32.94        22.62        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN 
       79.59        11.61        58.52       228.99        95.24       161.00 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z3 
      137.79       117.17       151.53        54.67        18.12        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       11.11         9.90        25.18        66.25        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH 
       53.92        65.92       215.44        15.68        10.16        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 
       17.29        52.01         8.65        94.98        33.73         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G 
      133.81        91.56       168.26        13.55        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       64.64        56.84        56.42        37.35       369.93       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       208.04        48.72        89.33 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       126.81        13.91        14.30        55.59 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       94.82        21.67       129.27        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       158.63 
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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B 
      109.58       148.08        31.40        35.44         9.17        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
       48.89        12.59        13.02       152.35       131.51       162.08 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25         8.88       148.18        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       31.27        32.05        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE 
       92.98       174.21        15.72       210.08        15.16        94.39 
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        19.30         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 
        2.04       139.89       117.93        10.13        32.48        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 
       12.62        50.10        59.41        65.88       294.77         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 
        0.69       212.22        63.02       105.04        24.03        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
        8.61        90.28        52.34         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
        2.20        10.36        15.16        36.03        14.43        93.07 
TCGA-Z2-AA3V 
       11.74 

$`DEL PEAK 19(10Q26.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       17.03        16.67        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JO 
       65.49        23.77       168.00        62.07        42.08        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A51E 
      130.72        46.98        46.32       166.52        13.87       174.84 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL 
       56.35        63.81       125.79        15.19       170.20        89.13 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-DA-A1HV 
       29.06       129.63         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        68.25         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        63.78         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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JD TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       71.21        51.62        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-FR-A7UA TCGA-FR-A8YC 
       79.99        23.34       247.04         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       29.46       216.92        28.08        48.85        53.52        40.27 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ 
        9.70        23.93        74.73       148.80        53.16        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
       77.82        50.14       174.84        12.43        49.45         0.20 
TCGA-FW-A3R5 TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       22.92         9.90        11.74        84.72        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A828 
       39.58        21.37       357.04         6.67        18.05       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
        4.01        42.08       219.16        38.56        56.98        59.41 
TCGA-WE-AAA0 TCGA-Z2-A8RT 
       30.18        23.64 

  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                          0.16                           0.20 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                        369.93                         357.04 
  DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE 
                         53.26                          47.69 
[1] "0.2 - 369.9 (53.3)" "0.2 - 357.0 (47.7)"
[1] "hr=" "1.2"
D41V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 19(10Q26.3) MUTATED                   36             5
  DEL PEAK 19(10Q26.3) WILD-TYPE                 25             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 19(10Q26.3) MUTATED                                          54
  DEL PEAK 19(10Q26.3) WILD-TYPE                                        18
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 19(10Q26.3) MUTATED                   130
  DEL PEAK 19(10Q26.3) WILD-TYPE                  79
D41V4, multiclass
                                           clus
vv                                          DEL PEAK 19(10Q26.3) MUTATED
  DISTANT METASTASIS                                                  36
  PRIMARY TUMOR                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           54
  REGIONAL LYMPH NODE                                                130
                                           clus
vv                                          DEL PEAK 19(10Q26.3) WILD-TYPE
  DISTANT METASTASIS                                                    25
  PRIMARY TUMOR                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             18
  REGIONAL LYMPH NODE                                                   79
[1] 4 2
[1] 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(10Q26.3) MUTATED             9       3      21       13       16
  DEL PEAK 19(10Q26.3) WILD-TYPE           3       4       7        4       11
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 19(10Q26.3) MUTATED         13         7        10         6
  DEL PEAK 19(10Q26.3) WILD-TYPE        9         7         9         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 19(10Q26.3) MUTATED          26         11         20         36
  DEL PEAK 19(10Q26.3) WILD-TYPE         9          4         12         22
                                vv
clus                             STAGE IV
  DEL PEAK 19(10Q26.3) MUTATED         14
  DEL PEAK 19(10Q26.3) WILD-TYPE        5
D41V5, multiclass
             clus
vv            DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  I OR II NOS                            9                              3
  STAGE 0                                3                              4
  STAGE I                               21                              7
  STAGE IA                              13                              4
  STAGE IB                              16                             11
  STAGE II                              13                              9
  STAGE IIA                              7                              7
  STAGE IIB                             10                              9
  STAGE IIC                              6                              6
  STAGE III                             26                              9
  STAGE IIIA                            11                              4
  STAGE IIIB                            20                             12
  STAGE IIIC                            36                             22
  STAGE IV                              14                              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(10Q26.3) MUTATED      44 51 40 45
  DEL PEAK 19(10Q26.3) WILD-TYPE    19 20 34 22
D41V6, multiclass
       clus
vv      DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  T0+T1                           44                             19
  T2                              51                             20
  T3                              40                             34
  T4                              45                             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                              N0  N1  N2  N3
  DEL PEAK 19(10Q26.3) MUTATED   104  45  24  29
  DEL PEAK 19(10Q26.3) WILD-TYPE  64  16  14  18
D41V7, multiclass
    clus
vv   DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  N0                          104                             64
  N1                           45                             16
  N2                           24                             14
  N3                           29                             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 19(10Q26.3) MUTATED   195   1   2   3   9
  DEL PEAK 19(10Q26.3) WILD-TYPE 111   3   1   1   0
D41V8, multiclass
     clus
vv    DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  M0                           195                            111
  M1                             1                              3
  M1A                            2                              1
  M1B                            3                              1
  M1C                            9                              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"
D41V9, binary
                                cls
clus                              0  1
  DEL PEAK 19(10Q26.3) MUTATED   79 55
  DEL PEAK 19(10Q26.3) WILD-TYPE 50 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED     79   55
  DEL PEAK 19(10Q26.3) WILD-TYPE   50   32
     clus
vv    DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  NO                            79                             50
  YES                           55                             32
[1] 2 2
[1] FALSE
D41V10, binary
                                cls
clus                               0   1
  DEL PEAK 19(10Q26.3) MUTATED    26 198
  DEL PEAK 19(10Q26.3) WILD-TYPE  17 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED     26  198
  DEL PEAK 19(10Q26.3) WILD-TYPE   17  106
     clus
vv    DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  NO                            26                             17
  YES                          198                            106
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, binary
                                cls
clus                               0   1
  DEL PEAK 19(10Q26.3) MUTATED    93 132
  DEL PEAK 19(10Q26.3) WILD-TYPE  38  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED     93  132
  DEL PEAK 19(10Q26.3) WILD-TYPE   38   85
        clus
vv       DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
  FEMALE                           93                             38
  MALE                            132                             85
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10Q26.3) MUTATED       1                         0   211
  DEL PEAK 19(10Q26.3) WILD-TYPE     4                         1   115
D41V13, multiclass
                           clus
vv                          DEL PEAK 19(10Q26.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              211
                           clus
vv                          DEL PEAK 19(10Q26.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                115
[1] 3 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 19(10Q26.3) MUTATED     4 217
  DEL PEAK 19(10Q26.3) WILD-TYPE   3 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q26.3) MUTATED      4  217
  DEL PEAK 19(10Q26.3) WILD-TYPE    3  117
                        clus
vv                       DEL PEAK 19(10Q26.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          217
                        clus
vv                       DEL PEAK 19(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            117
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 20(11P15.5) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(11P15.5) MUTATED    55  51
  DEL PEAK 20(11P15.5) WILD-TYPE 113 114
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           106                            227 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            51                            114 
$`DEL PEAK 20(11P15.5) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JD 
        6.97        16.47        32.42        10.29        85.32        11.41 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO 
       92.42        56.19        15.25        46.98        61.38         9.34 
TCGA-D3-A3MV TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       29.23        25.78        52.01        13.68        23.11        22.06 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A3Z3 
       10.22         4.18        75.65       124.47        87.62        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 
        5.72        11.31        48.79        35.80        39.19        44.52 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       25.15        17.56         0.20        23.15        19.00        13.35 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29L 
        1.35        60.23         4.34         1.18        37.97         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       39.62         9.50        12.03         8.09         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 
        8.09        36.30         9.67        60.00        28.31        98.27 
TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
       63.42        25.08        26.99        53.16         5.56       122.73 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH 
       30.15        15.95        21.60        21.60        16.14        21.73 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
       12.95        38.40         5.72         3.78         3.52        13.45 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       36.07         1.87         9.04         6.58        22.49         5.62 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1ZA TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       18.41        15.72         7.30        11.08        30.87        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       47.38        27.39        28.73        14.20        10.78         5.98 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U9 
        0.20        44.28        31.33        16.24        12.16        10.65 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZO 
       14.50        14.50        15.81         6.48        18.67        13.12 
TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT 
        5.36         1.94        12.07         8.22 

$`DEL PEAK 20(11P15.5) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        3.02         6.97         8.52       111.09        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        22.55        45.83        81.24         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        86.76        44.19         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
        6.31        64.44        59.57       114.67        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       13.32        24.00         6.31       103.59        26.37        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
      110.24        47.87        17.72        29.72        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      108.79        38.93        11.44         5.56        24.07         4.01 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.90        13.22        14.60        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-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
        7.00        14.83        13.15         0.13        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       11.57        10.55         6.31         8.12         1.12        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
        5.13         4.31        15.85         9.21         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29T 
       11.15        62.79         8.55        36.85         9.99        30.44 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       32.15        11.31        49.22        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        55.69         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33         8.84         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       29.46         2.73        44.25         7.96        14.56       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
      111.91        56.02        21.60        60.49        52.67       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         3.68        13.81        12.72         3.22        22.92 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 
       22.22         0.95        27.35        18.41        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       18.61        76.41        25.18        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88         4.21        28.60        42.84        34.68         9.57 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        6.58        17.72        78.44        11.80         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       12.62        11.74         1.71        85.74         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        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-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK 
        3.39        20.38         8.22        19.53         7.17        12.89 
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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4FC 
        0.82         5.23        53.85         3.22         7.36         6.41 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.99         0.13         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        7.23         0.85        11.61        84.72        10.13        15.42 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        14.50         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.33         0.69       164.19         8.98        60.03 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
        2.99        10.98       185.16        71.01        11.84         5.49 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
        7.10        21.07         3.72         3.42        21.83         1.08 
TCGA-WE-AAA0 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       19.96         6.18         4.70         6.67         5.98 

  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                          0.20                           0.13 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        124.47                         185.16 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        16.045                         14.240 
[1] "0.2 - 124.5 (16.0)" "0.1 - 185.2 (14.2)"
[1] "hr=" "1.1"
D42V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(11P15.5) MUTATED    56  52
  DEL PEAK 20(11P15.5) WILD-TYPE 117 114
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           108                            231 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            52                            114 
$`DEL PEAK 20(11P15.5) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JD 
       61.02        16.57       112.57        43.43       103.10        11.87 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO 
      171.58        56.19        58.06        46.98        86.93         9.34 
TCGA-D3-A3MV TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       45.30        26.89       135.75       178.32       125.19        79.59 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A149 
       11.61        58.52        95.24       161.00       137.79        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
        6.41        22.29        11.11        25.18        48.89        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SG 
      194.83       107.34        53.92       215.44        10.16        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I 
       54.02        17.29        14.70       133.81       151.27        13.55 
TCGA-EE-A29C TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       47.84         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GE 
       14.47        25.87        17.92        36.82        39.29       161.03 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
       75.48       129.27        96.23        47.54       248.65       162.48 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 
       53.26       122.73        54.51        23.47        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C 
       34.32       109.58        13.94        50.76         9.17        48.89 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3ET 
       12.59       131.51        37.25        23.34       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1ZA TCGA-FS-A1ZF 
       46.98         6.77        92.98        15.72        27.72        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F5 TCGA-FS-A4F8 
       32.75        47.38       101.26        49.48        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
       12.43        26.73         0.20       139.89       117.93        64.44 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-WE-A8K5 
       32.48        12.62        21.37        59.41        65.88        54.38 
TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT 
       90.28        59.41        43.73        10.36        15.16        23.64 

$`DEL PEAK 20(11P15.5) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       17.03        12.99        16.67       112.04        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        31.59        90.90        95.74        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        86.76        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
       12.10        66.08        59.57       130.72        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       60.23        24.53        13.87       103.59        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
      125.79       137.92        18.18        30.84        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      170.20        89.13        29.06       129.63       117.17       151.53 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        3.65        18.12        11.34         9.90        66.25        22.95 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
      117.21        20.38       176.55        35.93        61.18        65.92 
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-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.85        52.01         6.35        12.20        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        26.89        68.15         4.96 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       91.56       168.26        63.35        80.61        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       72.07        64.64        55.92       369.93       195.02        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH 
      102.90        86.14        59.28        67.43       314.56       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        89.33        54.74        79.66        90.97       126.81 
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-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       158.63       203.05       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
       43.23       134.40        71.21       124.31        51.62         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JB 
       13.81       138.81       172.18       127.20        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
       27.35        51.35       148.08        31.40        35.44        77.75 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       61.05        44.05       162.08        50.89         8.88       148.18 
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-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       33.21       174.21       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        29.46        94.39       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-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       53.52        40.27         9.70        23.93        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       77.82        50.14        66.67        49.45        77.88        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 
       11.74        84.72        10.13        62.79        39.58        46.36 
TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       50.10       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       212.22        63.02       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN 
      219.16       105.04        24.03        38.56         8.61        56.98 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3O 
       52.34         3.75        22.68         2.20        30.18        36.03 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        93.07        11.74 

  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                          0.20                           0.16 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        248.65                         369.93 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                         48.89                          51.35 
[1] "0.2 - 248.7 (48.9)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1.1"
D42V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 20(11P15.5) MUTATED                   16             1
  DEL PEAK 20(11P15.5) WILD-TYPE                 45             4
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 20(11P15.5) MUTATED                                          28
  DEL PEAK 20(11P15.5) WILD-TYPE                                        44
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 20(11P15.5) MUTATED                    64
  DEL PEAK 20(11P15.5) WILD-TYPE                 145
D42V4, multiclass
                                           clus
vv                                          DEL PEAK 20(11P15.5) MUTATED
  DISTANT METASTASIS                                                  16
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           28
  REGIONAL LYMPH NODE                                                 64
                                           clus
vv                                          DEL PEAK 20(11P15.5) WILD-TYPE
  DISTANT METASTASIS                                                    45
  PRIMARY TUMOR                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             44
  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
  DEL PEAK 20(11P15.5) MUTATED             5       1       9        4       10
  DEL PEAK 20(11P15.5) WILD-TYPE           7       6      19       13       17
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 20(11P15.5) MUTATED          2         2         4         5
  DEL PEAK 20(11P15.5) WILD-TYPE       20        12        15         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 20(11P15.5) MUTATED          14          4         11         24
  DEL PEAK 20(11P15.5) WILD-TYPE        21         11         21         34
                                vv
clus                             STAGE IV
  DEL PEAK 20(11P15.5) MUTATED          6
  DEL PEAK 20(11P15.5) WILD-TYPE       13
D42V5, multiclass
             clus
vv            DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  I OR II NOS                            5                              7
  STAGE 0                                1                              6
  STAGE I                                9                             19
  STAGE IA                               4                             13
  STAGE IB                              10                             17
  STAGE II                               2                             20
  STAGE IIA                              2                             12
  STAGE IIB                              4                             15
  STAGE IIC                              5                              7
  STAGE III                             14                             21
  STAGE IIIA                             4                             11
  STAGE IIIB                            11                             21
  STAGE IIIC                            24                             34
  STAGE IV                               6                             13
[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(11P15.5) MUTATED      20 24 17 26
  DEL PEAK 20(11P15.5) WILD-TYPE    43 47 57 41
D42V6, multiclass
       clus
vv      DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  T0+T1                           20                             43
  T2                              24                             47
  T3                              17                             57
  T4                              26                             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(11P15.5) MUTATED    43  25  12  16
  DEL PEAK 20(11P15.5) WILD-TYPE 125  36  26  31
D42V7, multiclass
    clus
vv   DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  N0                           43                            125
  N1                           25                             36
  N2                           12                             26
  N3                           16                             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 20(11P15.5) MUTATED    97   1   0   0   5
  DEL PEAK 20(11P15.5) WILD-TYPE 209   3   3   4   4
D42V8, multiclass
     clus
vv    DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  M0                            97                            209
  M1                             1                              3
  M1A                            0                              3
  M1B                            0                              4
  M1C                            5                              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"
D42V9, binary
                                cls
clus                              0  1
  DEL PEAK 20(11P15.5) MUTATED   37 35
  DEL PEAK 20(11P15.5) WILD-TYPE 92 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED     37   35
  DEL PEAK 20(11P15.5) WILD-TYPE   92   52
     clus
vv    DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  NO                            37                             92
  YES                           35                             52
[1] 2 2
[1] FALSE
D42V10, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED    11  98
  DEL PEAK 20(11P15.5) WILD-TYPE  32 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED     11   98
  DEL PEAK 20(11P15.5) WILD-TYPE   32  206
     clus
vv    DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  NO                            11                             32
  YES                           98                            206
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED    56  54
  DEL PEAK 20(11P15.5) WILD-TYPE  75 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED     56   54
  DEL PEAK 20(11P15.5) WILD-TYPE   75  163
        clus
vv       DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  FEMALE                           56                             75
  MALE                             54                            163
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(11P15.5) MUTATED       1                         0   103
  DEL PEAK 20(11P15.5) WILD-TYPE     4                         1   223
D42V13, multiclass
                           clus
vv                          DEL PEAK 20(11P15.5) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              103
                           clus
vv                          DEL PEAK 20(11P15.5) 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"
D42V14, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED     0 109
  DEL PEAK 20(11P15.5) WILD-TYPE   7 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED      0  109
  DEL PEAK 20(11P15.5) WILD-TYPE    7  225
                        clus
vv                       DEL PEAK 20(11P15.5) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                          109
                        clus
vv                       DEL PEAK 20(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            225
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 21(11Q23.3) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(11Q23.3) MUTATED   94 91
  DEL PEAK 21(11Q23.3) WILD-TYPE 74 74
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           185                            148 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                            91                             74 
$`DEL PEAK 21(11Q23.3) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB 
        6.97        16.47        32.42       110.79        22.55        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       10.29        85.32        68.22        86.76        11.41        44.19 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       92.42        56.19        64.44        15.25        46.98        61.38 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.00         6.31         9.34        26.37        29.23        93.21 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       52.01        13.68        17.72        23.11        29.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       10.22         4.18       142.45        75.65       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       11.44         5.56        21.93         9.90        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 
       14.60        48.79        35.80        39.19        44.52        25.15 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
        7.00        17.56        13.15         0.20        23.15        19.00 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20F 
       13.35        10.55         8.12         1.35        60.23        15.85 
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        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08        39.62         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 
       30.44         2.43        36.30         9.67        51.12        34.29 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2GU 
       60.00        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        53.16        52.67         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        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       36.07         6.58        17.72         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-A7U8 TCGA-FR-A7UA TCGA-FS-A1Z0 
       18.41        85.74        15.72         3.58        13.28        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF 
       14.24         7.33         7.30         3.39        19.53        11.08 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU 
       30.87        12.92        47.38         8.65        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         0.82         5.23         7.36        28.73        14.20 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        2.27         0.20         0.13        44.28        31.33        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK 
       16.24        15.42        12.16        14.70        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        14.50        15.81         0.43         5.79        18.05 
TCGA-RP-A694 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
        0.69        10.98        11.84         5.49         6.48        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       21.07        13.12         5.36         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
       12.07         6.18         4.70         8.22         5.98 

$`DEL PEAK 21(11Q23.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
        3.02         6.97         8.52       111.09        70.16        28.08 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH 
       45.83         8.38        21.14        88.50         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
        6.31        59.57       114.67        46.32        82.29        13.32 
TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      103.59        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GK 
       32.61        25.78       110.24        47.87        15.19       108.79 
TCGA-D3-A8GL TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1HY TCGA-DA-A1I0 
       38.93        24.07         4.01         5.72        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        36.69         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       19.36        14.83         0.13        13.22         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        6.31         1.12        12.20         5.13         4.31         4.34 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X 
        9.90        62.79         8.55        12.03        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL 
       11.31        49.22        36.33        17.98        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83        55.69         5.42        13.02        34.98 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        8.84         2.70         6.18        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A3AA 
        7.96        14.56       125.65        21.60        60.49       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB 
       51.62        13.81        12.72         3.22        22.92         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        18.41        33.60        18.61        38.40        76.41 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P 
       25.18        11.90       114.15        34.88         4.21        34.68 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A42K TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A8YC 
       78.44        11.80         5.62         6.71         5.36         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 
        4.70         3.29        64.47         3.45        11.01        15.52 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
       20.38         8.22         7.17        12.89        52.08         8.81 
TCGA-FS-A1ZS TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       49.15        53.85         3.22        10.78         5.98         6.41 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.99         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A824 
       11.61        84.72        11.84        11.05         0.33       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K6 
        8.98        60.03         2.99       185.16        71.01         7.10 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-Z2-AA3S 
        3.72         3.42        21.83         6.67 

  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                        142.45                         185.16 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                        15.250                         14.185 
[1] "0.1 - 142.4 (15.2)" "0.1 - 185.2 (14.2)"
[1] "hr=" "1"  
D43V2, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(11Q23.3) MUTATED   97 92
  DEL PEAK 21(11Q23.3) WILD-TYPE 76 74
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                           189                            150 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                            92                             74 
$`DEL PEAK 21(11Q23.3) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB 
       61.02        16.57       112.57       133.25        31.59        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       43.43       103.10       168.00        86.76        11.87        62.07 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
      171.58        56.19        66.08        58.06        46.98        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53        13.87         9.34        39.75        45.30       174.84 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      135.75       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       11.61        58.52       228.99        95.24       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       29.06       129.63       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 
       36.03       194.83       107.34        53.92        10.49       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17Y 
       13.87        10.16        68.25        54.02        17.29        27.22 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       94.98        14.70       133.81        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       63.35        47.84        13.97        64.64         2.60        56.84 
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       369.93        25.87 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       36.82        39.29        59.28        67.43       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MC 
       48.72        89.33        14.30        94.82       129.27        61.51 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       47.28        96.23       203.05       167.90        47.54       248.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        71.21        53.26       122.73         3.68        54.51 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH 
       23.47        36.95        64.08        34.32        53.19       109.58 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       31.40        13.94         9.17        48.89        12.59        26.37 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        61.05        44.05        50.89        37.25         8.88 
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-FR-A7UA TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       15.72        15.16        38.27       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       27.72        48.85        40.27        15.45        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26       133.55        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 
       27.02        66.67        28.73       174.84        77.88         0.20 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       47.54       139.89       117.93        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       32.48        39.58        12.62        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA1V 
       65.88       357.04         6.67        18.05         0.69        42.08 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        38.56        54.38        90.28        56.98        59.41 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        15.16        36.03 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
       14.43        23.64        11.74 

$`DEL PEAK 21(11Q23.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       17.03        12.99        16.67       112.04        71.80        28.08 
TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JH 
       90.90        65.49        23.77       115.53       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       12.10        59.57       130.72        46.32       166.52        60.23 
TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      103.59        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GK 
       63.81        26.89       125.79       137.92        15.19       170.20 
TCGA-D3-A8GL TCGA-D3-A8GS TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1HY 
       89.13       117.17        18.12        11.34        11.11       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       176.55        35.93        61.18        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
       68.09        28.60        15.68        17.85        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       12.20        29.82         8.65        33.73        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P 
        4.96       151.27        80.61        63.78        72.07        56.42 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD 
      195.02        17.92        46.82       102.90        86.14       314.56 
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       126.81        13.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       55.59        44.88        21.67        28.83        19.76       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MQ 
      268.73       103.20        16.96       204.66       158.63        43.23 
TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      134.40       124.31        51.62        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 
      127.20       201.80        27.35        51.35       148.08        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       50.76        77.75        98.40        13.02       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A42K TCGA-FR-A729 
        6.44       162.08        79.99        43.82         6.77       210.08 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
        7.00        34.82        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZK 
      228.59        28.08       357.37        53.52         9.70        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       74.73        11.41       148.80        77.82        50.14        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       26.73        49.45        22.92         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A4U8 TCGA-OD-A75X 
        7.23         2.04        11.74        84.72        46.36       294.77 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.33       212.22        63.02       121.08         4.01       219.16 
TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-Z2-AA3S 
      105.04         8.61        52.34         3.75        22.68        93.07 

  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                          0.20                           0.16 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                        369.93                         357.37 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                         47.84                          54.13 
[1] "0.2 - 369.9 (47.8)" "0.2 - 357.4 (54.1)"
[1] "hr=" "1.1"
D43V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 21(11Q23.3) MUTATED                   38             5
  DEL PEAK 21(11Q23.3) WILD-TYPE                 23             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 21(11Q23.3) MUTATED                                          37
  DEL PEAK 21(11Q23.3) WILD-TYPE                                        35
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 21(11Q23.3) MUTATED                   111
  DEL PEAK 21(11Q23.3) WILD-TYPE                  98
D43V4, multiclass
                                           clus
vv                                          DEL PEAK 21(11Q23.3) MUTATED
  DISTANT METASTASIS                                                  38
  PRIMARY TUMOR                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           37
  REGIONAL LYMPH NODE                                                111
                                           clus
vv                                          DEL PEAK 21(11Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                    23
  PRIMARY TUMOR                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             35
  REGIONAL LYMPH NODE                                                   98
[1] 4 2
[1] 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(11Q23.3) MUTATED             6       3      14       12       15
  DEL PEAK 21(11Q23.3) WILD-TYPE           6       4      14        5       12
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 21(11Q23.3) MUTATED         10         4        11         6
  DEL PEAK 21(11Q23.3) WILD-TYPE       12        10         8         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 21(11Q23.3) MUTATED          18         10         18         34
  DEL PEAK 21(11Q23.3) WILD-TYPE        17          5         14         24
                                vv
clus                             STAGE IV
  DEL PEAK 21(11Q23.3) MUTATED         11
  DEL PEAK 21(11Q23.3) WILD-TYPE        8
D43V5, multiclass
             clus
vv            DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  I OR II NOS                            6                              6
  STAGE 0                                3                              4
  STAGE I                               14                             14
  STAGE IA                              12                              5
  STAGE IB                              15                             12
  STAGE II                              10                             12
  STAGE IIA                              4                             10
  STAGE IIB                             11                              8
  STAGE IIC                              6                              6
  STAGE III                             18                             17
  STAGE IIIA                            10                              5
  STAGE IIIB                            18                             14
  STAGE IIIC                            34                             24
  STAGE IV                              11                              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(11Q23.3) MUTATED      38 35 40 37
  DEL PEAK 21(11Q23.3) WILD-TYPE    25 36 34 30
D43V6, multiclass
       clus
vv      DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  T0+T1                           38                             25
  T2                              35                             36
  T3                              40                             34
  T4                              37                             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
  DEL PEAK 21(11Q23.3) MUTATED   85 36 19 28
  DEL PEAK 21(11Q23.3) WILD-TYPE 83 25 19 19
D43V7, multiclass
    clus
vv   DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  N0                           85                             83
  N1                           36                             25
  N2                           19                             19
  N3                           28                             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
  DEL PEAK 21(11Q23.3) MUTATED   164   2   2   1   7
  DEL PEAK 21(11Q23.3) WILD-TYPE 142   2   1   3   2
D43V8, multiclass
     clus
vv    DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  M0                           164                            142
  M1                             2                              2
  M1A                            2                              1
  M1B                            1                              3
  M1C                            7                              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"
D43V9, binary
                                cls
clus                              0  1
  DEL PEAK 21(11Q23.3) MUTATED   76 51
  DEL PEAK 21(11Q23.3) WILD-TYPE 53 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED     76   51
  DEL PEAK 21(11Q23.3) WILD-TYPE   53   36
     clus
vv    DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  NO                            76                             53
  YES                           51                             36
[1] 2 2
[1] FALSE
D43V10, binary
                                cls
clus                               0   1
  DEL PEAK 21(11Q23.3) MUTATED    22 170
  DEL PEAK 21(11Q23.3) WILD-TYPE  21 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED     22  170
  DEL PEAK 21(11Q23.3) WILD-TYPE   21  134
     clus
vv    DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  NO                            22                             21
  YES                          170                            134
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, binary
                                cls
clus                               0   1
  DEL PEAK 21(11Q23.3) MUTATED    80 112
  DEL PEAK 21(11Q23.3) WILD-TYPE  51 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED     80  112
  DEL PEAK 21(11Q23.3) WILD-TYPE   51  105
        clus
vv       DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  FEMALE                           80                             51
  MALE                            112                            105
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11Q23.3) MUTATED       3                         1   176
  DEL PEAK 21(11Q23.3) WILD-TYPE     2                         0   150
D43V13, multiclass
                           clus
vv                          DEL PEAK 21(11Q23.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              176
                           clus
vv                          DEL PEAK 21(11Q23.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                150
[1] 3 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 21(11Q23.3) MUTATED     3 184
  DEL PEAK 21(11Q23.3) WILD-TYPE   4 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED      3  184
  DEL PEAK 21(11Q23.3) WILD-TYPE    4  150
                        clus
vv                       DEL PEAK 21(11Q23.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          184
                        clus
vv                       DEL PEAK 21(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            150
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 22(12Q23.3) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(12Q23.3) MUTATED    42  41
  DEL PEAK 22(12Q23.3) WILD-TYPE 126 124
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            83                            250 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            41                            124 
$`DEL PEAK 22(12Q23.3) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J7 TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 
        6.97        16.47        85.32        92.42        56.19        15.25 
TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR 
       61.38        29.23        54.31        21.44        47.87        13.68 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D9-A6EA TCGA-D9-A6EC 
       22.06         4.18        38.93       124.47        11.31        13.22 
TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29D 
       39.19        19.00        13.35        60.23         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        36.30        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       125.65        26.99 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
       53.16         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        18.41        33.60        31.40        12.95 
TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE 
        5.72        11.90        36.07         6.58         1.87         1.51 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA 
        1.71         5.62        85.74         3.45        15.52         7.30 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 
       30.87        47.38         8.65        40.64         3.22        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A268 
       10.78         5.98         0.99         0.13        16.24        15.42 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1V 
       14.50        15.81         0.43        11.05         0.33        10.98 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-Z2-A8RT 
       11.84        18.67         3.72        21.83         8.22 

$`DEL PEAK 22(12Q23.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         8.52       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.79        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP 
       44.19         7.50        36.16         6.31        64.44        59.57 
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-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59        26.37        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       31.30        32.28        32.61        25.78       110.24        52.01 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       17.72        23.11        29.72        10.22        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      108.79        75.65        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01        21.93         5.72         9.90        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        10.03        13.68         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-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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       23.15        13.22         0.20        11.57        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-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       62.79        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84        30.44         2.43        32.15        11.31        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.69        13.02        34.98         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46         2.73         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-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
       60.49        52.67       122.73        51.62        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
       12.72        22.92        21.60        16.14         0.95        27.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       21.73        18.61        38.40        76.41        25.18         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-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-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       11.80        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       22.49        18.41        15.72         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       13.28         2.20         4.70         3.29        64.47        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       23.80        14.24         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-A1ZP 
       19.53        11.08         7.17        12.92        12.89        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       53.85         7.36        14.20         6.41         2.27         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
       44.28        31.33        84.72        10.13        12.16        14.70 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O 
       11.84        10.65        14.50        14.50         5.79        18.05 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       164.19         8.98        60.03         2.99       185.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       71.01         5.49         6.48         7.10        21.07        13.12 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.42         5.36         1.08        19.96         1.94        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         4.70         6.67         5.98 

  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                        125.65                         185.16 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                         15.25                          14.65 
[1] "0.1 - 125.7 (15.2)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1"  
D44V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(12Q23.3) MUTATED    44  41
  DEL PEAK 22(12Q23.3) WILD-TYPE 129 125
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            85                            254 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                            41                            125 
$`DEL PEAK 22(12Q23.3) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J7 TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 
       12.99        16.57       103.10       171.58        56.19        58.06 
TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR 
       86.93        45.30       145.12        22.62       137.92       178.32 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A1X3 
       79.59        58.52        89.13       161.00       151.53        18.12 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A20B 
       25.18        66.25       194.83        54.02        17.29       133.81 
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 
       36.82       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 
      158.63       248.65       162.48        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        51.35       148.08 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T 
       31.40        13.94         9.17        13.02        37.25         8.88 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX 
       23.34        20.15        33.21         6.77       174.21        48.59 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       28.08        27.72        32.75       101.26       133.55        53.16 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU 
       50.14        28.73        12.43        26.73        22.92        47.54 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       64.44        62.79        21.37        65.88       357.04       294.77 
TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX 
        0.33        42.08        24.03        90.28        52.34        22.68 
TCGA-Z2-A8RT 
       23.64 

$`DEL PEAK 22(12Q23.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP 
       62.07       113.52        42.08        12.10        66.08        59.57 
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-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       56.35        32.94        63.81        26.89       125.79       135.75 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        11.61        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      170.20        95.24       137.79        29.06       129.63       117.17 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65         6.41        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        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-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-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.16        17.85        68.25        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       12.20        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H 
       14.70        26.89        68.15         4.96        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       13.55        63.35        80.61        47.84        63.78        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T 
        2.60        56.84        18.61        56.42        14.47       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
       25.87       195.02        46.82       102.90        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       314.56       161.03        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS 
       54.74        79.66        75.48        90.97       126.81        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       268.73        16.96       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      203.05       167.90        47.54        43.23       134.40        71.21 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
      122.73        51.62        13.81        23.47       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A195 
       36.95        34.32       201.80        27.35       109.58        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       50.76        77.75        98.40        48.89        12.59        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-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-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-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       210.08        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       29.46        94.39       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        47.38        23.93        74.73        11.41       148.80 
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-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
      174.84        49.45        77.88         0.20         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        10.13        32.48        39.58        46.36        12.62 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 
       50.10        59.41         6.67        18.05         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       63.02       121.08         4.01       219.16       105.04        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       54.38         8.61        56.98        59.41         3.75        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        30.18        10.36        15.16        36.03        14.43 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                          0.33                           0.16 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                        357.04                         369.93 
  DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE 
                         53.16                          49.17 
[1] "0.3 - 357.0 (53.2)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1.1"
D44V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 22(12Q23.3) MUTATED                   14             3
  DEL PEAK 22(12Q23.3) WILD-TYPE                 47             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 22(12Q23.3) MUTATED                                          22
  DEL PEAK 22(12Q23.3) WILD-TYPE                                        50
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 22(12Q23.3) MUTATED                    47
  DEL PEAK 22(12Q23.3) WILD-TYPE                 162
D44V4, multiclass
                                           clus
vv                                          DEL PEAK 22(12Q23.3) MUTATED
  DISTANT METASTASIS                                                  14
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           22
  REGIONAL LYMPH NODE                                                 47
                                           clus
vv                                          DEL PEAK 22(12Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                    47
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             50
  REGIONAL LYMPH NODE                                                  162
[1] 4 2
[1] 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(12Q23.3) MUTATED             4       2       7        4        6
  DEL PEAK 22(12Q23.3) WILD-TYPE           8       5      21       13       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 22(12Q23.3) MUTATED          6         2         4         3
  DEL PEAK 22(12Q23.3) WILD-TYPE       16        12        15         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 22(12Q23.3) MUTATED          12          4         10         11
  DEL PEAK 22(12Q23.3) WILD-TYPE        23         11         22         47
                                vv
clus                             STAGE IV
  DEL PEAK 22(12Q23.3) MUTATED          5
  DEL PEAK 22(12Q23.3) WILD-TYPE       14
D44V5, multiclass
             clus
vv            DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  I OR II NOS                            4                              8
  STAGE 0                                2                              5
  STAGE I                                7                             21
  STAGE IA                               4                             13
  STAGE IB                               6                             21
  STAGE II                               6                             16
  STAGE IIA                              2                             12
  STAGE IIB                              4                             15
  STAGE IIC                              3                              9
  STAGE III                             12                             23
  STAGE IIIA                             4                             11
  STAGE IIIB                            10                             22
  STAGE IIIC                            11                             47
  STAGE IV                               5                             14
[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(12Q23.3) MUTATED      14 18 16 21
  DEL PEAK 22(12Q23.3) WILD-TYPE    49 53 58 46
D44V6, multiclass
       clus
vv      DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  T0+T1                           14                             49
  T2                              18                             53
  T3                              16                             58
  T4                              21                             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(12Q23.3) MUTATED    40  20   9  11
  DEL PEAK 22(12Q23.3) WILD-TYPE 128  41  29  36
D44V7, multiclass
    clus
vv   DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  N0                           40                            128
  N1                           20                             41
  N2                            9                             29
  N3                           11                             36
[1] 4 2
[1] 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(12Q23.3) MUTATED    76   0   2   1   3
  DEL PEAK 22(12Q23.3) WILD-TYPE 230   4   1   3   6
D44V8, multiclass
     clus
vv    DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  M0                            76                            230
  M1                             0                              4
  M1A                            2                              1
  M1B                            1                              3
  M1C                            3                              6
[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 22(12Q23.3) MUTATED   31 23
  DEL PEAK 22(12Q23.3) WILD-TYPE 98 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED     31   23
  DEL PEAK 22(12Q23.3) WILD-TYPE   98   64
     clus
vv    DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  NO                            31                             98
  YES                           23                             64
[1] 2 2
[1] FALSE
D44V10, binary
                                cls
clus                               0   1
  DEL PEAK 22(12Q23.3) MUTATED    11  75
  DEL PEAK 22(12Q23.3) WILD-TYPE  32 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED     11   75
  DEL PEAK 22(12Q23.3) WILD-TYPE   32  229
     clus
vv    DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  NO                            11                             32
  YES                           75                            229
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, binary
                                cls
clus                               0   1
  DEL PEAK 22(12Q23.3) MUTATED    38  49
  DEL PEAK 22(12Q23.3) WILD-TYPE  93 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED     38   49
  DEL PEAK 22(12Q23.3) WILD-TYPE   93  168
        clus
vv       DEL PEAK 22(12Q23.3) MUTATED DEL PEAK 22(12Q23.3) WILD-TYPE
  FEMALE                           38                             93
  MALE                             49                            168
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(12Q23.3) MUTATED       0                         0    82
  DEL PEAK 22(12Q23.3) WILD-TYPE     5                         1   244
D44V13, multiclass
                           clus
vv                          DEL PEAK 22(12Q23.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               82
                           clus
vv                          DEL PEAK 22(12Q23.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                244
[1] 3 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 22(12Q23.3) MUTATED     0  85
  DEL PEAK 22(12Q23.3) WILD-TYPE   7 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(12Q23.3) MUTATED      0   85
  DEL PEAK 22(12Q23.3) WILD-TYPE    7  249
                        clus
vv                       DEL PEAK 22(12Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       DEL PEAK 22(12Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            249
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 23(13Q34) MUTATION ANALYSIS
D45V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 23(13Q34) MUTATED    40  37
  DEL PEAK 23(13Q34) WILD-TYPE 128 128
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          77                          256 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          37                          128 
$`DEL PEAK 23(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        86.76 
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       110.24        52.01 
TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z3 
       13.68        29.72       108.79         5.56        24.07        21.93 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       11.31        48.79        35.80        13.68         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A184 
       25.15         6.64        13.35        13.22         1.12         5.13 
TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T 
        1.18        11.15        62.79         9.50         8.09        30.44 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2M5 
       36.33        60.00        30.08        19.43        28.31         8.84 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
       44.25         7.96        60.49        53.16         5.56       122.73 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 
       30.15        12.72        21.60         0.95        21.73        31.40 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FS-A1ZA 
        9.57         6.58        12.62        18.41         5.36         7.30 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-GN-A266 TCGA-GN-A26D 
       30.87        12.92         7.36        10.78        10.13        14.70 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
       14.50        14.50         0.33         8.98        60.03        10.98 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-YG-AA3P 
       18.67         3.72         5.36         6.18         4.70 

$`DEL PEAK 23(13Q34) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       32.42        70.16       110.79        45.83        81.24        10.29 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        68.22        11.41        44.19         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
        6.31        56.19        64.44        59.57       114.67        15.25 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS 
       32.28        21.44        32.61        25.78        47.87        17.72 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       23.11        22.06        10.22        15.19         4.18       142.45 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A3Z1 
       38.93        75.65       124.47        87.62        11.44         4.01 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
        5.72         9.90        13.22        14.60        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       39.19        36.69         4.93        22.36        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        23.15 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       19.00         0.20        11.57        10.55         6.31         8.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
        1.35        12.20         4.31        60.23         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
        9.21         7.99         9.90        37.97         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        1.08        39.62        12.03         8.84         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL 
       51.12        34.29        17.98        47.21        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        55.69         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46         2.73        14.56        63.42       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA 
       56.02        25.08        26.99        21.60        52.67       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         3.68        13.81        15.95         3.22        22.92 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       21.60        16.14        22.22        27.35        18.41        33.60 
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-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-A19S 
        4.21        13.45        28.60        42.84        34.68        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-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       85.74        15.72         6.71         3.58        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.70         3.29        64.47         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-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       19.53        11.08         7.17        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         3.22        28.73        14.20 
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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       11.84        10.65        14.50        15.81         0.43        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1W 
        5.79        18.05         0.69       164.19         2.99       185.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
       71.01        11.84         5.49         6.48         7.10        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       13.12         3.42        21.83         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         8.22         6.67         5.98 

  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                        0.33                         0.13 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                      122.73                       185.16 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                      14.700                       14.715 
[1] "0.3 - 122.7 (14.7)" "0.1 - 185.2 (14.7)"
[1] "hr=" "1.1"
D45V2, survival
                              sevent
clus2                            0   1
  DEL PEAK 23(13Q34) MUTATED    42  37
  DEL PEAK 23(13Q34) WILD-TYPE 131 129
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          79                          260 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                          37                          129 
$`DEL PEAK 23(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        86.76 
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       125.79       135.75 
TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      178.32        30.84       170.20       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 
       54.67        22.29        25.18        48.89        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A5UL TCGA-EB-A5UN 
       35.93       107.34        53.92        68.09        17.29        52.01 
TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N 
       33.73        68.15        13.55        13.97        63.78        18.61 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       37.35       369.93        86.14       161.03        48.72        89.33 
TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A2MS 
       75.48        21.67       103.20        16.96       134.40       162.48 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JB 
       53.26       122.73        54.51       138.81        36.95       201.80 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2NG TCGA-FR-A3YN 
      109.58        31.40        50.89         8.88        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 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-A825 
       10.13        39.58        50.10        59.41         0.33        63.02 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O 
      121.08        42.08        90.28        52.34        43.73        36.03 
TCGA-YG-AA3P 
       14.43 

$`DEL PEAK 23(13Q34) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57        71.80       133.25        90.90        95.74        43.43 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       168.00        11.87        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.10        56.19        66.08        59.57       130.72        58.06 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS 
       32.94        22.62        63.81        26.89       137.92        18.18 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
      125.19        79.59        11.61        15.19        58.52       228.99 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A1JW 
       89.13        95.24       161.00       137.79        29.06         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC 
        6.41        18.12        11.34        11.11         9.90        66.25 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA 
       22.95       117.21        20.38       194.83        61.18        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 
       10.16        17.85        68.25        54.02         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        94.98        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        4.96       133.81       151.27        91.56       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       80.61        47.84        72.07        64.64         2.60        56.84 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        14.47        55.92        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        39.29        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
      314.56       208.04        54.74        79.66        90.97       126.81 
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-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      248.65        43.23        71.21       124.31        51.62         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        23.47       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19        27.35        51.35       148.08        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-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05       162.08        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21         6.77       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      210.08        15.16        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        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-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        50.14        28.73       174.84        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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        64.44        62.79        32.48        46.36        12.62 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       21.37        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        0.69       212.22         4.01       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       38.56        54.38         8.61        56.98        59.41         3.75 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT 
       22.68         2.20        30.18        10.36        15.16        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                        0.33                         0.16 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                      369.93                       357.37 
  DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE 
                       53.26                        48.87 
[1] "0.3 - 369.9 (53.3)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.1"
D45V3, continuous
                              vv
clus                           DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 23(13Q34) MUTATED                   12             2
  DEL PEAK 23(13Q34) WILD-TYPE                 49             3
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 23(13Q34) MUTATED                                          16
  DEL PEAK 23(13Q34) WILD-TYPE                                        56
                              vv
clus                           REGIONAL LYMPH NODE
  DEL PEAK 23(13Q34) MUTATED                    49
  DEL PEAK 23(13Q34) WILD-TYPE                 160
D45V4, multiclass
                                           clus
vv                                          DEL PEAK 23(13Q34) MUTATED
  DISTANT METASTASIS                                                12
  PRIMARY TUMOR                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                         16
  REGIONAL LYMPH NODE                                               49
                                           clus
vv                                          DEL PEAK 23(13Q34) WILD-TYPE
  DISTANT METASTASIS                                                  49
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           56
  REGIONAL LYMPH NODE                                                160
[1] 4 2
[1] 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(13Q34) MUTATED             2       1       7        6        6
  DEL PEAK 23(13Q34) WILD-TYPE          10       6      21       11       21
                              vv
clus                           STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 23(13Q34) MUTATED          6         4         3         3         9
  DEL PEAK 23(13Q34) WILD-TYPE       16        10        16         9        26
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 23(13Q34) MUTATED            2          9          9        6
  DEL PEAK 23(13Q34) WILD-TYPE         13         23         49       13
D45V5, multiclass
             clus
vv            DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  I OR II NOS                          2                           10
  STAGE 0                              1                            6
  STAGE I                              7                           21
  STAGE IA                             6                           11
  STAGE IB                             6                           21
  STAGE II                             6                           16
  STAGE IIA                            4                           10
  STAGE IIB                            3                           16
  STAGE IIC                            3                            9
  STAGE III                            9                           26
  STAGE IIIA                           2                           13
  STAGE IIIB                           9                           23
  STAGE IIIC                           9                           49
  STAGE IV                             6                           13
[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(13Q34) MUTATED      18 12 23 13
  DEL PEAK 23(13Q34) WILD-TYPE    45 59 51 54
D45V6, multiclass
       clus
vv      DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  T0+T1                         18                           45
  T2                            12                           59
  T3                            23                           51
  T4                            13                           54
[1] 4 2
[1] 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(13Q34) MUTATED    38  15  10   8
  DEL PEAK 23(13Q34) WILD-TYPE 130  46  28  39
D45V7, multiclass
    clus
vv   DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  N0                         38                          130
  N1                         15                           46
  N2                         10                           28
  N3                          8                           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                            M0  M1 M1A M1B M1C
  DEL PEAK 23(13Q34) MUTATED    68   0   1   2   4
  DEL PEAK 23(13Q34) WILD-TYPE 238   4   2   2   5
D45V8, multiclass
     clus
vv    DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  M0                          68                          238
  M1                           0                            4
  M1A                          1                            2
  M1B                          2                            2
  M1C                          4                            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"
D45V9, binary
                              cls
clus                            0  1
  DEL PEAK 23(13Q34) MUTATED   38 17
  DEL PEAK 23(13Q34) WILD-TYPE 91 70
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED     38   17
  DEL PEAK 23(13Q34) WILD-TYPE   91   70
     clus
vv    DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  NO                          38                           91
  YES                         17                           70
[1] 2 2
[1] FALSE
D45V10, binary
                              cls
clus                             0   1
  DEL PEAK 23(13Q34) MUTATED     8  71
  DEL PEAK 23(13Q34) WILD-TYPE  35 233
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED      8   71
  DEL PEAK 23(13Q34) WILD-TYPE   35  233
     clus
vv    DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  NO                           8                           35
  YES                         71                          233
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, binary
                              cls
clus                             0   1
  DEL PEAK 23(13Q34) MUTATED    28  51
  DEL PEAK 23(13Q34) WILD-TYPE 103 166
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED     28   51
  DEL PEAK 23(13Q34) WILD-TYPE  103  166
        clus
vv       DEL PEAK 23(13Q34) MUTATED DEL PEAK 23(13Q34) WILD-TYPE
  FEMALE                         28                          103
  MALE                           51                          166
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(13Q34) MUTATED       0                         0    74
  DEL PEAK 23(13Q34) WILD-TYPE     5                         1   252
D45V13, multiclass
                           clus
vv                          DEL PEAK 23(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             74
                           clus
vv                          DEL PEAK 23(13Q34) WILD-TYPE
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              252
[1] 3 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 23(13Q34) MUTATED     2  76
  DEL PEAK 23(13Q34) WILD-TYPE   5 258
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(13Q34) MUTATED      2   76
  DEL PEAK 23(13Q34) WILD-TYPE    5  258
                        clus
vv                       DEL PEAK 23(13Q34) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         76
                        clus
vv                       DEL PEAK 23(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          258
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 24(14Q23.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(14Q23.3) MUTATED    57  55
  DEL PEAK 24(14Q23.3) WILD-TYPE 111 110
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           112                            221 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                            55                            110 
$`DEL PEAK 24(14Q23.3) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JF 
        6.97        16.47       111.09        10.29        88.50        44.19 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
       56.19        64.44        59.57        61.38        13.32       103.59 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       29.23        54.31        21.44        52.01        47.87        13.68 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A6EA TCGA-DA-A1HV 
       22.06         4.18       124.47        24.07        11.31        48.79 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R 
       51.12        39.19        44.52        25.15        17.56         0.20 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29P 
       13.35        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        36.30         9.67        36.33        60.00 
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       125.65        25.08        21.60 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
       53.16       124.31        12.72         3.22        21.60        21.60 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       22.22         0.95        18.41        33.60        12.95         5.72 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19W 
       25.18        11.90       114.15        34.88        36.07        17.72 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 
        1.87         1.71         5.62        85.74         3.45        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM 
        7.33         7.30        20.38        19.53        30.87        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.65         8.81        40.64         3.22         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       14.20        10.78         0.13         7.23         0.85        11.61 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LL 
       31.33        16.24        15.42        12.16        10.65        14.50 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM 
        0.43        11.05         8.98        10.98        11.84        18.67 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-Z2-A8RT 
       21.83         5.36         6.18         8.22 

$`DEL PEAK 24(14Q23.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        3.02         6.97         8.52        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-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        68.22        86.76        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
        6.31        92.42       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       82.29        24.00         6.31         9.34        26.37        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.74        31.30        32.28        32.61        25.78       110.24 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       17.72        23.11        29.72        10.22        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      108.79        38.93        75.65        87.62        11.44         5.56 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01        21.93         5.72         9.90        13.22        14.60 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
       35.80        10.03        13.68         9.99        36.69         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13        23.15        19.00        13.22         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       60.23         4.34        15.85         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        9.90        11.15        62.79        36.85         1.08        39.62 
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        30.44        32.15 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GI 
       11.31        49.22        51.12        34.29        17.98        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        55.69 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME 
        1.15        13.02        34.98         8.84        47.51        29.46 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
        2.73        14.56        63.42       111.91        56.02        26.99 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       60.49        52.67         5.56       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD 
       30.15        13.81        15.95        22.92        16.14        27.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C 
       21.73        31.40        18.61        38.40        76.41         3.78 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        3.52        11.11         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       34.68         9.57         6.58        78.44        11.80         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       18.41        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        2.20         4.70         3.29        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-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
        5.23        53.85         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 
        0.99         0.16        17.33         9.90        44.28        84.72 
TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH 
       10.13        14.70        11.84        14.50        14.50        15.81 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        5.79        18.05         0.33         0.69       164.19        60.03 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
        2.99       185.16        71.01         5.49         6.48         7.10 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       21.07        13.12         3.72         3.42         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         4.70         6.67         5.98 

  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                        125.65                         185.16 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                        16.355                         14.500 
[1] "0.1 - 125.7 (16.4)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.1"
D46V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(14Q23.3) MUTATED    58  55
  DEL PEAK 24(14Q23.3) WILD-TYPE 115 111
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           113                            226 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                            55                            111 
$`DEL PEAK 24(14Q23.3) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JF 
       61.02        16.57       112.04        43.43       115.53        62.07 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
       56.19        66.08        59.57        86.93        60.23       103.59 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       45.30       145.12        22.62       135.75       137.92       178.32 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A6EA 
       79.59        58.52       161.00       117.17        54.67        25.18 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
       48.89       117.21       194.83       107.34        53.92       215.44 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G 
       10.16        17.29        27.22        33.73        47.84        72.07 
TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       56.42        25.87        17.92        36.82        39.29        86.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
      161.03       208.04        13.91        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN 
       19.76        47.28       103.20        16.96       158.63        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 
       43.23       162.48       124.31       138.81       172.18        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 
       64.08        53.19       201.80        51.35       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-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX 
      148.18        23.34        33.21         6.77       174.21        48.59 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH 
       28.08         7.79        27.72       357.37        40.27        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F4 
      101.26       133.55        11.41        53.16        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
       28.73       174.84        12.43        47.54         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 
       11.74       117.93        64.44        62.79        32.48        12.62 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ 
       21.37       357.04       294.77        63.02        42.08        24.03 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-Z2-A8RT 
       90.28        22.68        43.73        36.03        23.64 

$`DEL PEAK 24(14Q23.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       17.03        12.99        16.67       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-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       12.10       171.58       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
      166.52        24.53        13.87         9.34        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       55.73        56.35        32.94        63.81        26.89       125.79 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        11.61        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13        95.24       137.79        29.06       129.63 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53         3.65         6.41        18.12        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 
       11.11         9.90        66.25        22.95        36.03        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-A5KH TCGA-EB-A5SG 
       28.60        10.49        15.68        13.87        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       54.02        52.01         6.35        12.20        29.82         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       168.26        13.55        63.35        80.61 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        64.64         2.60        56.84        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       37.35        14.47        55.92       369.93       195.02        46.82 
TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ 
      102.90        59.28        67.43       314.56        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       54.74        79.66        75.48        90.97       126.81        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
       55.59        44.88        21.67        61.51       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MR 
      204.66        96.23       203.05       167.90       248.65       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH 
       13.81        23.47       127.20        34.32        27.35       109.58 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       31.40        35.44        50.76        77.75        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       26.37         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89         8.88        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-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       210.08        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       29.46        94.39       216.92       228.59       202.65        20.91 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       48.85        53.52        15.45         9.70        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       74.73       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       77.82        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        19.30         9.90       139.89        84.72        10.13 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS 
       39.58        46.36        50.10        59.41        65.88         6.67 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33         0.69       212.22       121.08         4.01 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
      219.16       105.04        38.56        54.38         8.61        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.41        52.34         3.75         2.20        30.18        10.36 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        14.43        93.07        11.74 

  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                          2.04                           0.16 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                        357.37                         369.93 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                         53.92                          48.87 
[1] "2.0 - 357.4 (53.9)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.2"
D46V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 24(14Q23.3) MUTATED                   20             1
  DEL PEAK 24(14Q23.3) WILD-TYPE                 41             4
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 24(14Q23.3) MUTATED                                          32
  DEL PEAK 24(14Q23.3) WILD-TYPE                                        40
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 24(14Q23.3) MUTATED                    62
  DEL PEAK 24(14Q23.3) WILD-TYPE                 147
D46V4, multiclass
                                           clus
vv                                          DEL PEAK 24(14Q23.3) MUTATED
  DISTANT METASTASIS                                                  20
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           32
  REGIONAL LYMPH NODE                                                 62
                                           clus
vv                                          DEL PEAK 24(14Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                    41
  PRIMARY TUMOR                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             40
  REGIONAL LYMPH NODE                                                  147
[1] 4 2
[1] 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(14Q23.3) MUTATED             5       0      12        4        7
  DEL PEAK 24(14Q23.3) WILD-TYPE           7       7      16       13       20
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 24(14Q23.3) MUTATED         10         3         4         5
  DEL PEAK 24(14Q23.3) WILD-TYPE       12        11        15         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 24(14Q23.3) MUTATED          14          5         12         19
  DEL PEAK 24(14Q23.3) WILD-TYPE        21         10         20         39
                                vv
clus                             STAGE IV
  DEL PEAK 24(14Q23.3) MUTATED          4
  DEL PEAK 24(14Q23.3) WILD-TYPE       15
D46V5, multiclass
             clus
vv            DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  I OR II NOS                            5                              7
  STAGE 0                                0                              7
  STAGE I                               12                             16
  STAGE IA                               4                             13
  STAGE IB                               7                             20
  STAGE II                              10                             12
  STAGE IIA                              3                             11
  STAGE IIB                              4                             15
  STAGE IIC                              5                              7
  STAGE III                             14                             21
  STAGE IIIA                             5                             10
  STAGE IIIB                            12                             20
  STAGE IIIC                            19                             39
  STAGE IV                               4                             15
[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(14Q23.3) MUTATED      24 26 21 23
  DEL PEAK 24(14Q23.3) WILD-TYPE    39 45 53 44
D46V6, multiclass
       clus
vv      DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  T0+T1                           24                             39
  T2                              26                             45
  T3                              21                             53
  T4                              23                             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
  DEL PEAK 24(14Q23.3) MUTATED    53  25   9  16
  DEL PEAK 24(14Q23.3) WILD-TYPE 115  36  29  31
D46V7, multiclass
    clus
vv   DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  N0                           53                            115
  N1                           25                             36
  N2                            9                             29
  N3                           16                             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 24(14Q23.3) MUTATED   104   0   1   0   3
  DEL PEAK 24(14Q23.3) WILD-TYPE 202   4   2   4   6
D46V8, multiclass
     clus
vv    DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  M0                           104                            202
  M1                             0                              4
  M1A                            1                              2
  M1B                            0                              4
  M1C                            3                              6
[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 24(14Q23.3) MUTATED   39 32
  DEL PEAK 24(14Q23.3) WILD-TYPE 90 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED     39   32
  DEL PEAK 24(14Q23.3) WILD-TYPE   90   55
     clus
vv    DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  NO                            39                             90
  YES                           32                             55
[1] 2 2
[1] FALSE
D46V10, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q23.3) MUTATED    15 100
  DEL PEAK 24(14Q23.3) WILD-TYPE  28 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED     15  100
  DEL PEAK 24(14Q23.3) WILD-TYPE   28  204
     clus
vv    DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  NO                            15                             28
  YES                          100                            204
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q23.3) MUTATED    49  67
  DEL PEAK 24(14Q23.3) WILD-TYPE  82 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED     49   67
  DEL PEAK 24(14Q23.3) WILD-TYPE   82  150
        clus
vv       DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  FEMALE                           49                             82
  MALE                             67                            150
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(14Q23.3) MUTATED       2                         0   108
  DEL PEAK 24(14Q23.3) WILD-TYPE     3                         1   218
D46V13, multiclass
                           clus
vv                          DEL PEAK 24(14Q23.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                              108
                           clus
vv                          DEL PEAK 24(14Q23.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                218
[1] 3 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 24(14Q23.3) MUTATED     2 110
  DEL PEAK 24(14Q23.3) WILD-TYPE   5 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED      2  110
  DEL PEAK 24(14Q23.3) WILD-TYPE    5  224
                        clus
vv                       DEL PEAK 24(14Q23.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          110
                        clus
vv                       DEL PEAK 24(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            224
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 25(14Q32.31) MUTATION ANALYSIS
D47V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(14Q32.31) MUTATED    57  53
  DEL PEAK 25(14Q32.31) WILD-TYPE 111 112
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                            110                             223 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                             53                             112 
$`DEL PEAK 25(14Q32.31) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JF 
        6.97        16.47       111.09        32.42        10.29        44.19 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
       56.19        64.44        59.57        61.38        13.32       103.59 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       29.23        54.31        21.44        52.01        47.87        13.68 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HY 
       22.06         4.18       124.47        11.31        48.79        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UL 
       39.19        44.52        25.15        17.56         0.20        13.35 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29V 
       10.55         1.12        37.97        62.79         8.55         2.43 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GJ 
       36.30         9.67        36.33        51.12        60.00        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       125.65        25.08        53.16 
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-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
        0.95        18.41        33.60        12.95         5.72        25.18 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE 
       11.90       114.15        34.88        36.07         1.87         1.51 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        1.71         5.62        85.74         3.45        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        7.30        20.38        19.53        30.87        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        8.81        40.64         3.22        28.73        14.20        10.78 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 
        0.13         7.23         0.85        11.61        31.33        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X 
       15.42        12.16        10.65        14.50         0.43        11.05 
TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY 
        0.33        10.98        11.84        18.67        21.83         5.36 
TCGA-YG-AA3O TCGA-Z2-A8RT 
        6.18         8.22 

$`DEL PEAK 25(14Q32.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        3.02         6.97         8.52        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        81.24        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        86.76        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
        6.31        92.42       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       82.29        24.00         6.31         9.34        26.37        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.74        31.30        32.28        32.61        25.78       110.24 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       17.72        23.11        29.72        10.22        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      108.79        38.93        75.65        87.62        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC 
       24.07         4.01        21.93         5.72         9.90        13.22 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       14.60        35.80        10.03        13.68         9.99        36.69 
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-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       13.15         0.13        23.15        19.00        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57         6.31         8.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        7.99         9.90        11.15        36.85         1.08        39.62 
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        30.44 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD 
       32.15         8.09        11.31        49.22        34.29        17.98 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        30.08        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2ME 
       55.69         1.15        13.02        34.98         8.84        29.46 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
        2.73        14.56        63.42       111.91        56.02        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       21.60        60.49        52.67         5.56       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 
        3.68        30.15        13.81        15.95        22.92        16.14 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        21.73        31.40        18.61        38.40        76.41 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        3.78         3.52        11.11         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57         6.58        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       11.80        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       22.49        18.41        15.72         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       13.28         2.20         4.70         3.29        64.47        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
       23.80        14.24         3.39         8.22        11.08         7.17 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
       12.92        12.89        52.08        49.15         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC 
        0.82         5.23        53.85         7.36         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.99         0.16        17.33         9.90 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LL 
       44.28        84.72        10.13        14.70        11.84        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 
       14.50        15.81         5.79        18.05         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
        8.98        60.03         2.99       185.16        71.01         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        6.48         7.10        21.07        13.12         3.72         3.42 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
        1.08        19.96         1.94        12.07         4.70         6.67 
TCGA-Z2-AA3V 
        5.98 

  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                           0.13                            0.13 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                         125.65                          185.16 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                         17.015                          14.500 
[1] "0.1 - 125.7 (17.0)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.1"
D47V2, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(14Q32.31) MUTATED    58  53
  DEL PEAK 25(14Q32.31) WILD-TYPE 115 113
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                            111                             228 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                             53                             113 
$`DEL PEAK 25(14Q32.31) MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A2JF 
       61.02        16.57       112.04       112.57        43.43        62.07 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR 
       56.19        66.08        59.57        86.93        60.23       103.59 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       45.30       145.12        22.62       135.75       137.92       178.32 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D9-A149 TCGA-D9-A6EA TCGA-DA-A1HV 
       79.59        58.52       161.00        54.67        25.18        48.89 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R 
      117.21       194.83       107.34        53.92       215.44        10.16 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       17.29        27.22        33.73        47.84        63.78        72.07 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       25.87        36.82        39.29        86.14        59.28       161.03 
TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       89.33        13.91        94.82       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN 
       61.51        47.28       103.20        16.96       158.63        47.54 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
      162.48       124.31       138.81       172.18        36.95        64.08 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       53.19       201.80        51.35       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-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 
       20.15        33.21         6.77       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-A4F5 TCGA-FS-A4F8 
      133.55        11.41        53.16        50.14        28.73       174.84 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 
       12.43        47.54         7.23         2.04        11.74       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB 
       64.44        62.79        32.48        12.62        50.10       357.04 
TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZX 
      294.77         0.33        42.08        24.03        90.28        22.68 
TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-Z2-A8RT 
       43.73        36.03        23.64 

$`DEL PEAK 25(14Q32.31) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       17.03        12.99        16.67        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       12.10       171.58       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
      166.52        24.53        13.87         9.34        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       55.73        56.35        32.94        63.81        26.89       125.79 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        11.61        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13        95.24       137.79        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17       151.53         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       22.29        11.11         9.90        66.25        22.95        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       176.55        35.93        61.18        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       68.09        28.60        10.49        15.68        13.87        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        54.02        52.01         6.35        12.20        29.82 
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-A20I TCGA-EE-A29A 
      133.81       151.27        91.56       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        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       56.42        37.35        14.47        55.92       369.93       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH 
       17.92        46.82       102.90        67.43       314.56       208.04 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        54.74        79.66        75.48        90.97       126.81 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2ME TCGA-EE-A2MF 
       14.30        55.59        44.88        21.67       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66        96.23       203.05       167.90       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      134.40        71.21        53.26       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD 
       54.51        13.81        23.47       127.20        34.32        27.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C 
      109.58        31.40        35.44        50.76        77.75        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       12.59        26.37         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18        79.99        43.82 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       92.98        15.72       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       34.82        29.46        94.39       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       20.91        48.85        53.52        15.45         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       23.93        74.73       148.80        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       27.02        77.82        66.67        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 
        0.20        22.92         0.16        19.30         9.90       139.89 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-GN-A9SD 
       84.72        10.13        39.58        46.36        21.37        59.41 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       65.88         6.67        18.05         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
      121.08         4.01       219.16       105.04        38.56        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
        8.61        56.98        59.41        52.34         3.75         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       30.18        10.36        15.16        14.43        93.07        11.74 

  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                           0.33                            0.16 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                         357.37                          369.93 
  DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE 
                          53.19                           48.87 
[1] "0.3 - 357.4 (53.2)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.2"
D47V3, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 25(14Q32.31) MUTATED                   21             1
  DEL PEAK 25(14Q32.31) WILD-TYPE                 40             4
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 25(14Q32.31) MUTATED                                          29
  DEL PEAK 25(14Q32.31) WILD-TYPE                                        43
                                 vv
clus                              REGIONAL LYMPH NODE
  DEL PEAK 25(14Q32.31) MUTATED                    63
  DEL PEAK 25(14Q32.31) WILD-TYPE                 146
D47V4, multiclass
                                           clus
vv                                          DEL PEAK 25(14Q32.31) MUTATED
  DISTANT METASTASIS                                                   21
  PRIMARY TUMOR                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            29
  REGIONAL LYMPH NODE                                                  63
                                           clus
vv                                          DEL PEAK 25(14Q32.31) WILD-TYPE
  DISTANT METASTASIS                                                     40
  PRIMARY TUMOR                                                           4
  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
  DEL PEAK 25(14Q32.31) MUTATED             7       1      11        5        7
  DEL PEAK 25(14Q32.31) WILD-TYPE           5       6      17       12       20
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 25(14Q32.31) MUTATED          9         2         4         3
  DEL PEAK 25(14Q32.31) WILD-TYPE       13        12        15         9
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 25(14Q32.31) MUTATED          14          3         14         19
  DEL PEAK 25(14Q32.31) WILD-TYPE        21         12         18         39
                                 vv
clus                              STAGE IV
  DEL PEAK 25(14Q32.31) MUTATED          5
  DEL PEAK 25(14Q32.31) WILD-TYPE       14
D47V5, multiclass
             clus
vv            DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  I OR II NOS                             7                               5
  STAGE 0                                 1                               6
  STAGE I                                11                              17
  STAGE IA                                5                              12
  STAGE IB                                7                              20
  STAGE II                                9                              13
  STAGE IIA                               2                              12
  STAGE IIB                               4                              15
  STAGE IIC                               3                               9
  STAGE III                              14                              21
  STAGE IIIA                              3                              12
  STAGE IIIB                             14                              18
  STAGE IIIC                             19                              39
  STAGE IV                                5                              14
[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(14Q32.31) MUTATED      25 24 20 21
  DEL PEAK 25(14Q32.31) WILD-TYPE    38 47 54 46
D47V6, multiclass
       clus
vv      DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  T0+T1                            25                              38
  T2                               24                              47
  T3                               20                              54
  T4                               21                              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 25(14Q32.31) MUTATED    52  26   8  16
  DEL PEAK 25(14Q32.31) WILD-TYPE 116  35  30  31
D47V7, multiclass
    clus
vv   DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  N0                            52                             116
  N1                            26                              35
  N2                             8                              30
  N3                            16                              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 25(14Q32.31) MUTATED   102   0   1   0   4
  DEL PEAK 25(14Q32.31) WILD-TYPE 204   4   2   4   5
D47V8, multiclass
     clus
vv    DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  M0                            102                             204
  M1                              0                               4
  M1A                             1                               2
  M1B                             0                               4
  M1C                             4                               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"
D47V9, binary
                                 cls
clus                               0  1
  DEL PEAK 25(14Q32.31) MUTATED   39 30
  DEL PEAK 25(14Q32.31) WILD-TYPE 90 57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED     39   30
  DEL PEAK 25(14Q32.31) WILD-TYPE   90   57
     clus
vv    DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  NO                             39                              90
  YES                            30                              57
[1] 2 2
[1] FALSE
D47V10, binary
                                 cls
clus                                0   1
  DEL PEAK 25(14Q32.31) MUTATED    16  98
  DEL PEAK 25(14Q32.31) WILD-TYPE  27 206
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED     16   98
  DEL PEAK 25(14Q32.31) WILD-TYPE   27  206
     clus
vv    DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  NO                             16                              27
  YES                            98                             206
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, binary
                                 cls
clus                                0   1
  DEL PEAK 25(14Q32.31) MUTATED    44  71
  DEL PEAK 25(14Q32.31) WILD-TYPE  87 146
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED     44   71
  DEL PEAK 25(14Q32.31) WILD-TYPE   87  146
        clus
vv       DEL PEAK 25(14Q32.31) MUTATED DEL PEAK 25(14Q32.31) WILD-TYPE
  FEMALE                            44                              87
  MALE                              71                             146
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(14Q32.31) MUTATED       2                         0   107
  DEL PEAK 25(14Q32.31) WILD-TYPE     3                         1   219
D47V13, multiclass
                           clus
vv                          DEL PEAK 25(14Q32.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                               107
                           clus
vv                          DEL PEAK 25(14Q32.31) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                 219
[1] 3 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 25(14Q32.31) MUTATED     2 110
  DEL PEAK 25(14Q32.31) WILD-TYPE   5 224
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(14Q32.31) MUTATED      2  110
  DEL PEAK 25(14Q32.31) WILD-TYPE    5  224
                        clus
vv                       DEL PEAK 25(14Q32.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           110
                        clus
vv                       DEL PEAK 25(14Q32.31) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             224
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 26(15Q13.3) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(15Q13.3) MUTATED    31  46
  DEL PEAK 26(15Q13.3) WILD-TYPE 137 119
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            77                            256 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            46                            119 
$`DEL PEAK 26(15Q13.3) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A3C6 TCGA-D3-A3CC 
        6.97        16.47        81.24        85.32        15.25        61.38 
TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GC 
        6.31        26.37        32.61        52.01        47.87        22.06 
TCGA-D3-A8GN TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
      124.47        13.22        48.79        35.80        51.12        39.19 
TCGA-DA-A1I8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 
       25.15         0.20         0.13        19.00         6.31         8.12 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GP 
        1.08        12.03         8.09         9.67        47.21         5.42 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
        8.84        47.51         9.53         2.73         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 
      125.65        56.02        52.67         5.56       122.73         3.22 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 
       21.60        22.22        18.41        31.40        12.95         5.72 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NE TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 
        6.58        17.72         1.51        22.49         3.45        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A4F8 
       15.52        19.53         7.17        12.89        47.38        14.20 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 
        5.98         2.27         0.20         0.13         0.16        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       10.13        16.24        14.70        10.65        14.50        14.50 
TCGA-OD-A75X TCGA-RP-A694 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZQ 
       11.05         0.69        10.98        11.84         3.72 

$`DEL PEAK 26(15Q13.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         8.52       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J8 
      110.79        28.08        22.55        45.83        10.29         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        86.76        11.41        44.19 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       59.57       114.67        46.98        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       24.00         9.34       103.59        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       31.30        54.31        32.28        21.44        25.78       110.24 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
       13.68        17.72        23.11        29.72        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
        4.18       142.45       108.79        38.93        75.65        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       11.44         5.56        24.07         4.01        21.93         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.90        11.31        14.60        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        36.69         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UL 
        7.00        17.56        14.83        13.15        23.15        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       13.22         0.20        11.57        10.55         1.12         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        60.23         4.34        15.85 
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 
       62.79         8.55        36.85        39.62         9.50         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        36.30        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       60.00        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83        55.69         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        60.49        53.16 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31        51.62         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
       12.72        22.92        21.60        16.14         0.95        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       21.73        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-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       11.74         9.04         6.58         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       85.74        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        2.20         4.70         3.29        64.47        11.01        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
        7.33         7.30         3.39        20.38         8.22        11.08 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        12.92        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
        3.22         7.36        28.73        10.78         6.41         0.99 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-HR-A2OH 
       84.72        15.42        12.16        11.84        14.50        15.81 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
        0.43         5.79        18.05         0.33       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       60.03         2.99       185.16        71.01         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
        7.10        18.67        21.07        13.12         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36         1.08        19.96         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                          0.13                           0.20 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                        125.65                         185.16 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                         14.50                          15.57 
[1] "0.1 - 125.7 (14.5)" "0.2 - 185.2 (15.6)"
[1] "hr=" "1.4"
D48V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(15Q13.3) MUTATED    32  47
  DEL PEAK 26(15Q13.3) WILD-TYPE 141 119
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            79                            260 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                            47                            119 
$`DEL PEAK 26(15Q13.3) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A3C6 TCGA-D3-A3CC 
       12.99        16.57        95.74       103.10        58.06        86.93 
TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GC 
       13.87        39.75        63.81       135.75       137.92        79.59 
TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
      161.00       151.53         6.41        66.25        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
      117.21       194.83        53.92        10.16        17.85        54.02 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 
        8.65        94.98         2.60        56.42        37.35        39.29 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF 
      208.04        13.91        21.67        61.51        47.28       268.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU 
       16.96       204.66       158.63       167.90        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A193 
      122.73       172.18        64.08        53.19        51.35        31.40 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NE TCGA-ER-A3EV 
       13.94         9.17         8.88       148.18        20.15        46.98 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK 
       48.59       202.65        28.08        40.27         9.70        23.93 
TCGA-FS-A1ZM TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
      101.26       174.84        26.73        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 
        0.16       117.93        10.13        64.44        39.58        12.62 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A694 TCGA-W3-AA1V TCGA-WE-A8JZ 
       50.10        21.37       294.77         0.69        42.08        24.03 
TCGA-WE-A8ZQ 
       52.34 

$`DEL PEAK 26(15Q13.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J8 
      133.25        28.08        31.59        90.90        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        86.76        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       59.57       130.72        46.98        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34       103.59        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        22.62        26.89       125.79 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
      178.32        18.18       125.19        30.84        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       58.52       228.99       170.20        89.13        95.24       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 
       29.06       129.63       117.17        54.67         3.65        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       11.34        22.29        11.11         9.90        25.18        22.95 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       20.38       176.55        35.93       107.34        61.18        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-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        68.25        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82        27.22        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       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        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       64.64        56.84        18.61        14.47        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       86.14        59.28        67.43       314.56       161.03        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       126.81 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
       19.76       103.27       103.20        96.23       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC 
      248.65        43.23       134.40       162.48       124.31        51.62 
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-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        34.32       201.80        27.35       109.58       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-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      210.08        15.16         7.00        38.27        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       94.39       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-A1ZJ 
       48.85       357.37        53.52        15.45        32.75        47.38 
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-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT 
       28.73        12.43        49.45        22.92        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 
        7.23         2.04        11.74       139.89        84.72        62.79 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       32.48        46.36        59.41        65.88       357.04         6.67 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33       212.22        63.02       121.08         4.01 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      219.16       105.04        38.56        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       56.98        59.41         3.75        22.68        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       30.18        10.36        15.16        36.03        14.43        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                          0.16                           0.33 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                        294.77                         369.93 
  DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE 
                         50.10                          50.45 
[1] "0.2 - 294.8 (50.1)" "0.3 - 369.9 (50.5)"
[1] "hr=" "1.3"
D48V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 26(15Q13.3) MUTATED                   14             2
  DEL PEAK 26(15Q13.3) WILD-TYPE                 47             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 26(15Q13.3) MUTATED                                          15
  DEL PEAK 26(15Q13.3) WILD-TYPE                                        57
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 26(15Q13.3) MUTATED                    49
  DEL PEAK 26(15Q13.3) WILD-TYPE                 160
D48V4, multiclass
                                           clus
vv                                          DEL PEAK 26(15Q13.3) MUTATED
  DISTANT METASTASIS                                                  14
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           15
  REGIONAL LYMPH NODE                                                 49
                                           clus
vv                                          DEL PEAK 26(15Q13.3) WILD-TYPE
  DISTANT METASTASIS                                                    47
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             57
  REGIONAL LYMPH NODE                                                  160
[1] 4 2
[1] 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(15Q13.3) MUTATED             1       2      10        2        6
  DEL PEAK 26(15Q13.3) WILD-TYPE          11       5      18       15       21
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 26(15Q13.3) MUTATED          4         2         4         5
  DEL PEAK 26(15Q13.3) WILD-TYPE       18        12        15         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 26(15Q13.3) MUTATED          11          5          7         11
  DEL PEAK 26(15Q13.3) WILD-TYPE        24         10         25         47
                                vv
clus                             STAGE IV
  DEL PEAK 26(15Q13.3) MUTATED          4
  DEL PEAK 26(15Q13.3) WILD-TYPE       15
D48V5, multiclass
             clus
vv            DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  I OR II NOS                            1                             11
  STAGE 0                                2                              5
  STAGE I                               10                             18
  STAGE IA                               2                             15
  STAGE IB                               6                             21
  STAGE II                               4                             18
  STAGE IIA                              2                             12
  STAGE IIB                              4                             15
  STAGE IIC                              5                              7
  STAGE III                             11                             24
  STAGE IIIA                             5                             10
  STAGE IIIB                             7                             25
  STAGE IIIC                            11                             47
  STAGE IV                               4                             15
[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(15Q13.3) MUTATED      14 18 11 24
  DEL PEAK 26(15Q13.3) WILD-TYPE    49 53 63 43
D48V6, multiclass
       clus
vv      DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  T0+T1                           14                             49
  T2                              18                             53
  T3                              11                             63
  T4                              24                             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 26(15Q13.3) MUTATED    40  11   9  11
  DEL PEAK 26(15Q13.3) WILD-TYPE 128  50  29  36
D48V7, multiclass
    clus
vv   DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  N0                           40                            128
  N1                           11                             50
  N2                            9                             29
  N3                           11                             36
[1] 4 2
[1] 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(15Q13.3) MUTATED    70   1   1   1   2
  DEL PEAK 26(15Q13.3) WILD-TYPE 236   3   2   3   7
D48V8, multiclass
     clus
vv    DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  M0                            70                            236
  M1                             1                              3
  M1A                            1                              2
  M1B                            1                              3
  M1C                            2                              7
[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 26(15Q13.3) MUTATED   31 20
  DEL PEAK 26(15Q13.3) WILD-TYPE 98 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED     31   20
  DEL PEAK 26(15Q13.3) WILD-TYPE   98   67
     clus
vv    DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  NO                            31                             98
  YES                           20                             67
[1] 2 2
[1] FALSE
D48V10, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q13.3) MUTATED     9  72
  DEL PEAK 26(15Q13.3) WILD-TYPE  34 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED      9   72
  DEL PEAK 26(15Q13.3) WILD-TYPE   34  232
     clus
vv    DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  NO                             9                             34
  YES                           72                            232
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q13.3) MUTATED    29  52
  DEL PEAK 26(15Q13.3) WILD-TYPE 102 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED     29   52
  DEL PEAK 26(15Q13.3) WILD-TYPE  102  165
        clus
vv       DEL PEAK 26(15Q13.3) MUTATED DEL PEAK 26(15Q13.3) WILD-TYPE
  FEMALE                           29                            102
  MALE                             52                            165
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(15Q13.3) MUTATED       2                         0    77
  DEL PEAK 26(15Q13.3) WILD-TYPE     3                         1   249
D48V13, multiclass
                           clus
vv                          DEL PEAK 26(15Q13.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               77
                           clus
vv                          DEL PEAK 26(15Q13.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                249
[1] 3 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 26(15Q13.3) MUTATED     0  80
  DEL PEAK 26(15Q13.3) WILD-TYPE   7 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q13.3) MUTATED      0   80
  DEL PEAK 26(15Q13.3) WILD-TYPE    7  254
                        clus
vv                       DEL PEAK 26(15Q13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           80
                        clus
vv                       DEL PEAK 26(15Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            254
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 27(15Q21.1) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q21.1) MUTATED    34  49
  DEL PEAK 27(15Q21.1) WILD-TYPE 134 116
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            83                            250 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            49                            116 
$`DEL PEAK 27(15Q21.1) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML 
        6.97        16.47        81.24        15.25        61.38         6.31 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GC 
       26.37        32.28        32.61        52.01        47.87        22.06 
TCGA-D3-A8GD TCGA-D3-A8GN TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
       10.22       124.47        13.22        48.79        35.80        39.19 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       25.15         4.93        13.15         0.20         0.13        19.00 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29L TCGA-EE-A29P 
        6.31         8.12         1.12        12.20         1.08        12.03 
TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.09         9.67        47.21         8.84        47.51         9.53 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU 
        2.73         7.96        14.56       125.65        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        18.41        31.40 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19J 
       12.95        38.40         5.72         3.78       114.15         4.21 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A8YD TCGA-FS-A1YX 
        6.58        17.72         6.58        22.49         4.70         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A4F8 
       23.80        15.52         7.17        47.38        40.64        14.20 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        2.27         0.13         0.16        31.33        10.13        16.24 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH 
       12.16        14.70        10.65        14.50        14.50        15.81 
TCGA-OD-A75X TCGA-RP-A694 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZQ 
       11.05         0.69        10.98        11.84         3.72 

$`DEL PEAK 27(15Q21.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         8.52       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        28.08        22.55        45.83        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       64.44        59.57       114.67        46.98        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         9.34       103.59        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       54.74        31.30        54.31        21.44        25.78       110.24 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GI 
       13.68        17.72        23.11        29.72        15.19         4.18 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      142.45       108.79        38.93        75.65        87.62        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        5.56        24.07         4.01        21.93         5.72         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       11.31        14.60        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       44.52        36.69        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
       17.56        14.83        23.15        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       11.57        10.55         1.35         5.13         4.31        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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-A29M 
       37.97        11.15        62.79         8.55        36.85        39.62 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        9.50         8.84         9.99        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        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        55.69         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-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       29.46        44.25        63.42       111.91        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
       21.60        60.49        53.16        52.67       124.31        51.62 
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-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14         0.95        27.35        21.73        33.60 
TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       18.61        76.41        25.18         3.52        11.90        11.11 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       36.07        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       12.62        11.74         9.04         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       85.74        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        2.20         3.29        64.47        11.01        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-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.92        12.89        52.08         8.65         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-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        3.22         7.36        28.73        10.78         5.98         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.20         0.99        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A9SD 
       11.61        44.28        84.72        15.42        11.84        14.50 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 
        0.43         5.79        18.05         0.33       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       60.03         2.99       185.16        71.01         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
        7.10        18.67        21.07        13.12         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36         1.08        19.96         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                          0.13                           0.20 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                        125.65                         185.16 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                         13.22                          15.90 
[1] "0.1 - 125.7 (13.2)" "0.2 - 185.2 (15.9)"
[1] "hr=" "1.5"
D49V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q21.1) MUTATED    35  49
  DEL PEAK 27(15Q21.1) WILD-TYPE 138 117
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            84                            255 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                            49                            117 
$`DEL PEAK 27(15Q21.1) MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1QB TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3ML 
       12.99        16.57        95.74        58.06        86.93        13.87 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GC 
       39.75        32.94        63.81       135.75       137.92        79.59 
TCGA-D3-A8GD TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       11.61       161.00       151.53        66.25        48.89        36.03 
TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
      194.83        53.92        65.92        13.87        10.16        17.85 
TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29L 
       54.02         8.65        94.98        33.73        26.89         2.60 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MC 
       56.42        37.35        39.29       208.04        21.67        61.51 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
       47.28       268.73        16.96       204.66       158.63       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        51.35 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19G 
       31.40        13.94        50.76         9.17        48.89       268.93 
TCGA-ER-A19J TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A8YD 
        6.44         8.88       148.18        80.32        46.98        29.46 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT 
       48.59       202.65        28.08         9.70       101.26        53.16 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A266 
      174.84        77.88        47.54         0.16       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       64.44        32.48        39.58        12.62        50.10        21.37 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A694 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZQ 
       65.88       294.77         0.69        42.08        24.03        52.34 

$`DEL PEAK 27(15Q21.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        31.59        90.90        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08        59.57       130.72        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53         9.34       103.59        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       55.73        56.35       145.12        22.62        26.89       125.79 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GI 
      178.32        18.18       125.19        30.84        15.19        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      228.99       170.20        89.13        95.24       137.79        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17        54.67         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       11.34        22.29        11.11         9.90        25.18        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-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-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       27.22        14.70        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        72.07        64.64        56.84        18.61 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        55.92       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03        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       126.81        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       44.88        94.82       129.27        28.83        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      103.20        96.23       203.05        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      134.40       162.48        71.21       124.31        51.62         3.68 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32       201.80        27.35       109.58       148.08        35.44 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       77.75        98.40        12.59        13.02        26.37       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-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-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       210.08        15.16         7.00        38.27        34.82 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       94.39       216.92       228.59        20.91         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH 
       48.85       357.37        53.52        40.27        15.45        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       66.67        28.73        12.43        26.73        49.45         0.20 
TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       22.92        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-LH-A9QB 
      139.89        84.72        62.79        46.36        59.41       357.04 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        6.67        18.05         0.33       212.22        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
        4.01       219.16       105.04        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       90.28        56.98        59.41         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        30.18        10.36        15.16        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                          0.16                           0.20 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                        294.77                         369.93 
  DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE 
                         50.43                          50.14 
[1] "0.2 - 294.8 (50.4)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.3"
D49V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 27(15Q21.1) MUTATED                   14             2
  DEL PEAK 27(15Q21.1) WILD-TYPE                 47             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 27(15Q21.1) MUTATED                                          17
  DEL PEAK 27(15Q21.1) WILD-TYPE                                        55
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 27(15Q21.1) MUTATED                    53
  DEL PEAK 27(15Q21.1) WILD-TYPE                 156
D49V4, multiclass
                                           clus
vv                                          DEL PEAK 27(15Q21.1) MUTATED
  DISTANT METASTASIS                                                  14
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           17
  REGIONAL LYMPH NODE                                                 53
                                           clus
vv                                          DEL PEAK 27(15Q21.1) WILD-TYPE
  DISTANT METASTASIS                                                    47
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             55
  REGIONAL LYMPH NODE                                                  156
[1] 4 2
[1] 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(15Q21.1) MUTATED             2       2      11        2        5
  DEL PEAK 27(15Q21.1) WILD-TYPE          10       5      17       15       22
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 27(15Q21.1) MUTATED          4         2         4         5
  DEL PEAK 27(15Q21.1) WILD-TYPE       18        12        15         7
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 27(15Q21.1) MUTATED          11          7          9         11
  DEL PEAK 27(15Q21.1) WILD-TYPE        24          8         23         47
                                vv
clus                             STAGE IV
  DEL PEAK 27(15Q21.1) MUTATED          4
  DEL PEAK 27(15Q21.1) WILD-TYPE       15
D49V5, multiclass
             clus
vv            DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  I OR II NOS                            2                             10
  STAGE 0                                2                              5
  STAGE I                               11                             17
  STAGE IA                               2                             15
  STAGE IB                               5                             22
  STAGE II                               4                             18
  STAGE IIA                              2                             12
  STAGE IIB                              4                             15
  STAGE IIC                              5                              7
  STAGE III                             11                             24
  STAGE IIIA                             7                              8
  STAGE IIIB                             9                             23
  STAGE IIIC                            11                             47
  STAGE IV                               4                             15
[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(15Q21.1) MUTATED      14 18 14 22
  DEL PEAK 27(15Q21.1) WILD-TYPE    49 53 60 45
D49V6, multiclass
       clus
vv      DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  T0+T1                           14                             49
  T2                              18                             53
  T3                              14                             60
  T4                              22                             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 27(15Q21.1) MUTATED    40  12  11  13
  DEL PEAK 27(15Q21.1) WILD-TYPE 128  49  27  34
D49V7, multiclass
    clus
vv   DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  N0                           40                            128
  N1                           12                             49
  N2                           11                             27
  N3                           13                             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 27(15Q21.1) MUTATED    76   1   1   1   2
  DEL PEAK 27(15Q21.1) WILD-TYPE 230   3   2   3   7
D49V8, multiclass
     clus
vv    DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  M0                            76                            230
  M1                             1                              3
  M1A                            1                              2
  M1B                            1                              3
  M1C                            2                              7
[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 27(15Q21.1) MUTATED   33 21
  DEL PEAK 27(15Q21.1) WILD-TYPE 96 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED     33   21
  DEL PEAK 27(15Q21.1) WILD-TYPE   96   66
     clus
vv    DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  NO                            33                             96
  YES                           21                             66
[1] 2 2
[1] FALSE
D49V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q21.1) MUTATED     9  78
  DEL PEAK 27(15Q21.1) WILD-TYPE  34 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED      9   78
  DEL PEAK 27(15Q21.1) WILD-TYPE   34  226
     clus
vv    DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  NO                             9                             34
  YES                           78                            226
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q21.1) MUTATED    36  51
  DEL PEAK 27(15Q21.1) WILD-TYPE  95 166
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED     36   51
  DEL PEAK 27(15Q21.1) WILD-TYPE   95  166
        clus
vv       DEL PEAK 27(15Q21.1) MUTATED DEL PEAK 27(15Q21.1) WILD-TYPE
  FEMALE                           36                             95
  MALE                             51                            166
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(15Q21.1) MUTATED       3                         0    81
  DEL PEAK 27(15Q21.1) WILD-TYPE     2                         1   245
D49V13, multiclass
                           clus
vv                          DEL PEAK 27(15Q21.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               81
                           clus
vv                          DEL PEAK 27(15Q21.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                245
[1] 3 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 27(15Q21.1) MUTATED     1  84
  DEL PEAK 27(15Q21.1) WILD-TYPE   6 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q21.1) MUTATED      1   84
  DEL PEAK 27(15Q21.1) WILD-TYPE    6  250
                        clus
vv                       DEL PEAK 27(15Q21.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 27(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            250
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 28(16P13.3) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(16P13.3) MUTATED    30  28
  DEL PEAK 28(16P13.3) WILD-TYPE 138 137
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            58                            275 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            28                            137 
$`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-D3-A8GD 
       64.44       114.67        61.38        32.28        21.44        10.22 
TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EB-A5UL 
       75.65        13.22        35.80        13.68         0.20        13.35 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
        8.12         1.12         1.18        11.15         1.08        39.62 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GU 
       32.15         8.09        11.31        34.29        55.69        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU 
        8.84        98.27       125.65        56.02        21.60         5.56 
TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
      122.73        21.60        22.22        33.60        31.40        12.95 
TCGA-ER-A19E TCGA-ER-A19T TCGA-FS-A1Z0 TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU 
       11.90         6.58        23.80         8.22        40.64         8.68 
TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A26D 
       27.39         0.99         0.13        44.28        16.24        14.70 
TCGA-OD-A75X TCGA-WE-A8K5 TCGA-YG-AA3P TCGA-Z2-A8RT 
       11.05         6.48         4.70         8.22 

$`DEL PEAK 28(16P13.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      110.79        28.08        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        88.50        86.76        11.41        44.19         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       36.16         6.31        56.19        59.57        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-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       54.31        32.61        25.78       110.24        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE 
       13.68        17.72        23.11        29.72        22.06        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
        4.18       142.45       108.79        38.93       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       11.44         5.56        24.07         4.01        21.93         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        11.31        14.60        48.79        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19         9.99        44.52        36.69        25.15         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-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       13.15         0.13        23.15        19.00        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57        10.55         6.31         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        4.31        60.23         4.34        15.85         9.21         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
        9.90        37.97        62.79         8.55        36.85         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        30.44         2.43 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83         5.42         1.15        13.02        34.98 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
       44.25         7.96        14.56        63.42       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
       26.99        60.49        53.16        52.67       124.31        51.62 
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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       22.92        21.60        16.14         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       21.73        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        11.01        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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.15         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-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.20         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
       11.61        31.33        84.72        10.13        15.42        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       11.84        10.65        14.50        14.50        14.50        15.81 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.43         5.79        18.05         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        8.98        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       11.84         5.49         7.10        18.67        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
        3.72         3.42        21.83         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         6.18         6.67         5.98 

  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        125.65                         185.16 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                          21.6                           14.5 
[1] "0.1 - 125.7 (21.6)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.2"
D50V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(16P13.3) MUTATED    30  28
  DEL PEAK 28(16P13.3) WILD-TYPE 143 138
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            58                            281 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            28                            138 
$`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-D3-A8GD 
       66.08       130.72        86.93        32.94        22.62        11.61 
TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EB-A5UL 
       95.24        66.25        36.03       176.55        10.16        17.29 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
       94.98        33.73        13.55        13.97         2.60        56.84 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GU 
      195.02        17.92        46.82        67.43       126.81        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU 
       21.67       129.27       158.63       167.90        43.23        53.26 
TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
      122.73        36.95        53.19       148.08        31.40        13.94 
TCGA-ER-A19E TCGA-ER-A19T TCGA-FS-A1Z0 TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU 
       13.02         8.88       202.65        53.52        53.16        26.56 
TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A26D 
       49.48        22.92        47.54       139.89        64.44        39.58 
TCGA-OD-A75X TCGA-WE-A8K5 TCGA-YG-AA3P TCGA-Z2-A8RT 
      294.77        54.38        14.43        23.64 

$`DEL PEAK 28(16P13.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       115.53        86.76        11.87        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       42.08        12.10        56.19        59.57        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-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
      145.12        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE 
      178.32        18.18       125.19        30.84        79.59        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       58.52       228.99       170.20        89.13       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        6.41        18.12        11.34        22.29        11.11         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-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-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       17.85        68.25        54.02        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82        27.22         8.65        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        4.96       133.81       151.27        91.56       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       80.61        47.84        63.78        72.07        64.64        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       369.93        25.87 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      102.90        36.82        39.29        86.14        59.28       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
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       134.40       162.48        71.21       124.31        51.62 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        64.08        34.32       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      109.58        35.44        50.76         9.17        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-A19S 
      131.51        61.05        44.05       162.08        50.89        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-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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       210.08        15.16 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        7.00        38.27        34.82        29.46        94.39       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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
       11.74       117.93        84.72        10.13        62.79        32.48 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       46.36        12.62        50.10        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      357.04         6.67        18.05         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
       63.02       121.08         4.01        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        38.56         8.61        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       52.34         3.75        22.68        43.73         2.20        30.18 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       10.36        15.16        36.03        93.07        11.74 

  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                         369.93 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        53.225                         49.450 
[1] "2.6 - 294.8 (53.2)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D50V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 28(16P13.3) MUTATED                    9             2
  DEL PEAK 28(16P13.3) WILD-TYPE                 52             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 28(16P13.3) MUTATED                                           9
  DEL PEAK 28(16P13.3) WILD-TYPE                                        63
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 28(16P13.3) MUTATED                    39
  DEL PEAK 28(16P13.3) WILD-TYPE                 170
D50V4, multiclass
                                           clus
vv                                          DEL PEAK 28(16P13.3) MUTATED
  DISTANT METASTASIS                                                   9
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            9
  REGIONAL LYMPH NODE                                                 39
                                           clus
vv                                          DEL PEAK 28(16P13.3) WILD-TYPE
  DISTANT METASTASIS                                                    52
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             63
  REGIONAL LYMPH NODE                                                  170
[1] 4 2
[1] 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           9       5      24       14       22
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 28(16P13.3) MUTATED          2         2         6         3
  DEL PEAK 28(16P13.3) WILD-TYPE       20        12        13         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 28(16P13.3) MUTATED           7          3          6          6
  DEL PEAK 28(16P13.3) WILD-TYPE        28         12         26         52
                                vv
clus                             STAGE IV
  DEL PEAK 28(16P13.3) MUTATED          5
  DEL PEAK 28(16P13.3) WILD-TYPE       14
D50V5, multiclass
             clus
vv            DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  I OR II NOS                            3                              9
  STAGE 0                                2                              5
  STAGE I                                4                             24
  STAGE IA                               3                             14
  STAGE IB                               5                             22
  STAGE II                               2                             20
  STAGE IIA                              2                             12
  STAGE IIB                              6                             13
  STAGE IIC                              3                              9
  STAGE III                              7                             28
  STAGE IIIA                             3                             12
  STAGE IIIB                             6                             26
  STAGE IIIC                             6                             52
  STAGE IV                               5                             14
[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 14 10 15
  DEL PEAK 28(16P13.3) WILD-TYPE    56 57 64 52
D50V6, multiclass
       clus
vv      DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  T0+T1                            7                             56
  T2                              14                             57
  T3                              10                             64
  T4                              15                             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 28(16P13.3) MUTATED    33  10   7   6
  DEL PEAK 28(16P13.3) WILD-TYPE 135  51  31  41
D50V7, multiclass
    clus
vv   DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  N0                           33                            135
  N1                           10                             51
  N2                            7                             31
  N3                            6                             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                              M0  M1 M1A M1B M1C
  DEL PEAK 28(16P13.3) MUTATED    52   0   1   0   4
  DEL PEAK 28(16P13.3) WILD-TYPE 254   4   2   4   5
D50V8, multiclass
     clus
vv    DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  M0                            52                            254
  M1                             0                              4
  M1A                            1                              2
  M1B                            0                              4
  M1C                            4                              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 28(16P13.3) MUTATED    25  17
  DEL PEAK 28(16P13.3) WILD-TYPE 104  70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED     25   17
  DEL PEAK 28(16P13.3) WILD-TYPE  104   70
     clus
vv    DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  NO                            25                            104
  YES                           17                             70
[1] 2 2
[1] FALSE
D50V10, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED     2  58
  DEL PEAK 28(16P13.3) WILD-TYPE  41 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED      2   58
  DEL PEAK 28(16P13.3) WILD-TYPE   41  246
     clus
vv    DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  NO                             2                             41
  YES                           58                            246
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED    28  32
  DEL PEAK 28(16P13.3) WILD-TYPE 103 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED     28   32
  DEL PEAK 28(16P13.3) WILD-TYPE  103  185
        clus
vv       DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  FEMALE                           28                            103
  MALE                             32                            185
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(16P13.3) MUTATED       1                         1    57
  DEL PEAK 28(16P13.3) WILD-TYPE     4                         0   269
D50V13, multiclass
                           clus
vv                          DEL PEAK 28(16P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               57
                           clus
vv                          DEL PEAK 28(16P13.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                269
[1] 3 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 28(16P13.3) MUTATED     3  57
  DEL PEAK 28(16P13.3) WILD-TYPE   4 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED      3   57
  DEL PEAK 28(16P13.3) WILD-TYPE    4  277
                        clus
vv                       DEL PEAK 28(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK 28(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            277
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 29(16Q12.1) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16Q12.1) MUTATED    52  55
  DEL PEAK 29(16Q12.1) WILD-TYPE 116 110
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                           107                            226 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            55                            110 
$`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 
       86.76        44.19        92.42        56.19        64.44       114.67 
TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI 
       61.38        21.44        17.72        22.06        10.22         4.18 
TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
       75.65        21.93        13.22        35.80        13.68         9.99 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A17Z 
       17.56        14.83         0.20        23.15        13.35         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B 
        8.12         1.12         4.31         4.34         1.18         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       37.97        11.15         1.08        39.62         9.50        12.03 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH 
       32.15         8.09        11.31         9.67        34.29        47.21 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK 
       55.69         5.42         8.84         9.53        63.42       125.65 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
       56.02        25.08        21.60        53.16         5.56       122.73 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI 
       30.15        13.81        22.92        21.60        22.22        33.60 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19N TCGA-ER-A19T 
       31.40        12.95        25.18        11.90        42.84         6.58 
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         0.85        44.28        31.33 
TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       16.24        14.70        14.50         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       18.05         2.99        11.84         6.48         3.72        21.83 
TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94         6.18         4.70         6.67         5.98 

$`DEL PEAK 29(16Q12.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        22.55        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-A2JP 
       88.50        11.41         7.50        36.16         6.31        59.57 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       15.25        46.98        46.32        82.29        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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       54.74        31.30        54.31        32.28        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB 
      110.24        52.01        47.87        13.68        23.11        29.72 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       15.19       142.45       108.79        38.93       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 
       11.44         5.56        24.07         4.01         5.72         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        14.60        48.79        51.12        10.03        39.19 
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-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN 
       19.36         7.00        13.15         0.13        19.00        13.22 
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-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29G 
       60.23        15.85         9.21         7.99        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       36.85         8.09         8.84         9.99        30.44         2.43 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       49.22        36.30        36.33        51.12        17.98        60.00 
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-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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51        29.46         2.73        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
       14.56       111.91        26.99        60.49        52.67       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       51.62         3.68        15.95        12.72         3.22        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
       16.14         0.95        27.35        18.41        21.73        18.61 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       38.40         5.72        76.41         3.78         3.52        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
      114.15        34.88         4.21        13.45        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        9.57        36.07        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        1.71         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        3.58         5.36        13.28         2.20         4.70         3.29 
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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       20.38         8.22        19.53         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY 
       12.89        47.38         8.65         8.81        49.15         0.82 
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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 
        6.41         2.27         0.16        17.33         9.90        11.61 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        10.13        15.42        12.16        11.84        10.65 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       14.50        14.50        15.81         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
        8.98        60.03        10.98       185.16        71.01         5.49 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
        7.10        18.67        21.07        13.12         3.42         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT 
        1.08        19.96        12.07         8.22 

  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                        125.65                         185.16 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                         14.50                          15.22 
[1] "0.1 - 125.7 (14.5)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.1"
D51V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16Q12.1) MUTATED    54  55
  DEL PEAK 29(16Q12.1) WILD-TYPE 119 111
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                           109                            230 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                            55                            111 
$`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 
       86.76        62.07       171.58        56.19        66.08       130.72 
TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI 
       86.93        22.62        18.18        79.59        11.61        58.52 
TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HW 
       95.24       151.53        54.67        22.29        66.25        36.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG 
      176.55        35.93       215.44        15.68        10.16        68.25 
TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C 
       17.29         8.65        94.98        33.73         4.96       151.27 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
       13.55        80.61        47.84        13.97         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 
       18.61        56.42       195.02        17.92        46.82        39.29 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MD 
       67.43       208.04       126.81        13.91        21.67        47.28 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS 
       96.23       158.63       167.90        47.54        43.23       162.48 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 
       53.26       122.73        54.51        13.81       127.20        36.95 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19E 
       53.19       148.08        31.40        13.94        98.40        13.02 
TCGA-ER-A19N TCGA-ER-A19T TCGA-ER-A19W TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       44.05         8.88       148.18       202.65        27.72        48.85 
TCGA-FS-A1ZF TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 
       15.45        74.73        53.16        26.56        49.48        50.14 
TCGA-FS-A4F4 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
       66.67         0.20        22.92        47.54         7.23         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A8LK TCGA-LH-A9QB 
      139.89       117.93        64.44        39.58        50.10       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K5 
      294.77         6.67        18.05         4.01        24.03        54.38 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       52.34        22.68        10.36        36.03        14.43        93.07 
TCGA-Z2-AA3V 
       11.74 

$`DEL PEAK 29(16Q12.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        31.59        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-A2JP 
      115.53        11.87       113.52        42.08        12.10        59.57 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98        46.32       166.52        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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35       145.12        32.94        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB 
      125.79       135.75       137.92       178.32       125.19        30.84 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       15.19       228.99       170.20        89.13       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
       29.06       129.63       117.17         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       11.34        11.11         9.90        25.18        22.95        48.89 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      117.21        20.38       194.83       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q 
       65.92        23.44        68.09        28.60        10.49        13.87 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       17.85        54.02        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F 
       27.22        14.70        26.89        68.15       133.81        91.56 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q 
      168.26        63.35        63.78        72.07        64.64        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        55.92       369.93        25.87       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28       314.56       161.03        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML 
      103.27       268.73       103.20        16.96       204.66       203.05 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      248.65       134.40        71.21       124.31        51.62         3.68 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       23.47       138.81       172.18        64.08        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       27.35        51.35       109.58        35.44        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        48.89        12.59        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05       162.08        50.89        37.25 
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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59        20.91        28.08         7.79       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       40.27         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      133.55        11.41       148.80        27.09        27.02        77.82 
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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 
        0.16        19.30         9.90        11.74        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       62.79        32.48        46.36        12.62        21.37        59.41 
TCGA-HR-A2OH TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       65.88         0.33         0.69       212.22        63.02       121.08 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       42.08       219.16       105.04        38.56         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       56.98        59.41         3.75        43.73         2.20        30.18 
TCGA-WE-AAA4 TCGA-Z2-A8RT 
       15.16        23.64 

  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 
                        357.04                         369.93 
  DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE 
                        50.140                         50.105 
[1] "0.2 - 357.0 (50.1)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.1"
D51V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 29(16Q12.1) MUTATED                   18             2
  DEL PEAK 29(16Q12.1) WILD-TYPE                 43             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 29(16Q12.1) MUTATED                                          17
  DEL PEAK 29(16Q12.1) WILD-TYPE                                        55
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 29(16Q12.1) MUTATED                    73
  DEL PEAK 29(16Q12.1) WILD-TYPE                 136
D51V4, multiclass
                                           clus
vv                                          DEL PEAK 29(16Q12.1) MUTATED
  DISTANT METASTASIS                                                  18
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           17
  REGIONAL LYMPH NODE                                                 73
                                           clus
vv                                          DEL PEAK 29(16Q12.1) WILD-TYPE
  DISTANT METASTASIS                                                    43
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             55
  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 29(16Q12.1) MUTATED             4       3       5        7        9
  DEL PEAK 29(16Q12.1) WILD-TYPE           8       4      23       10       18
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 29(16Q12.1) MUTATED          7         3         9         6
  DEL PEAK 29(16Q12.1) WILD-TYPE       15        11        10         6
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 29(16Q12.1) MUTATED          11          3         10         15
  DEL PEAK 29(16Q12.1) WILD-TYPE        24         12         22         43
                                vv
clus                             STAGE IV
  DEL PEAK 29(16Q12.1) MUTATED          7
  DEL PEAK 29(16Q12.1) WILD-TYPE       12
D51V5, multiclass
             clus
vv            DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  I OR II NOS                            4                              8
  STAGE 0                                3                              4
  STAGE I                                5                             23
  STAGE IA                               7                             10
  STAGE IB                               9                             18
  STAGE II                               7                             15
  STAGE IIA                              3                             11
  STAGE IIB                              9                             10
  STAGE IIC                              6                              6
  STAGE III                             11                             24
  STAGE IIIA                             3                             12
  STAGE IIIB                            10                             22
  STAGE IIIC                            15                             43
  STAGE IV                               7                             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
  DEL PEAK 29(16Q12.1) MUTATED      19 19 20 25
  DEL PEAK 29(16Q12.1) WILD-TYPE    44 52 54 42
D51V6, multiclass
       clus
vv      DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  T0+T1                           19                             44
  T2                              19                             52
  T3                              20                             54
  T4                              25                             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 29(16Q12.1) MUTATED    57  17  11  14
  DEL PEAK 29(16Q12.1) WILD-TYPE 111  44  27  33
D51V7, multiclass
    clus
vv   DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  N0                           57                            111
  N1                           17                             44
  N2                           11                             27
  N3                           14                             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                              M0  M1 M1A M1B M1C
  DEL PEAK 29(16Q12.1) MUTATED    93   1   1   1   5
  DEL PEAK 29(16Q12.1) WILD-TYPE 213   3   2   3   4
D51V8, multiclass
     clus
vv    DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  M0                            93                            213
  M1                             1                              3
  M1A                            1                              2
  M1B                            1                              3
  M1C                            5                              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"
D51V9, binary
                                cls
clus                              0  1
  DEL PEAK 29(16Q12.1) MUTATED   46 29
  DEL PEAK 29(16Q12.1) WILD-TYPE 83 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED     46   29
  DEL PEAK 29(16Q12.1) WILD-TYPE   83   58
     clus
vv    DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  NO                            46                             83
  YES                           29                             58
[1] 2 2
[1] FALSE
D51V10, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED    13  98
  DEL PEAK 29(16Q12.1) WILD-TYPE  30 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED     13   98
  DEL PEAK 29(16Q12.1) WILD-TYPE   30  206
     clus
vv    DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  NO                            13                             30
  YES                           98                            206
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED    46  65
  DEL PEAK 29(16Q12.1) WILD-TYPE  85 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED     46   65
  DEL PEAK 29(16Q12.1) WILD-TYPE   85  152
        clus
vv       DEL PEAK 29(16Q12.1) MUTATED DEL PEAK 29(16Q12.1) WILD-TYPE
  FEMALE                           46                             85
  MALE                             65                            152
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16Q12.1) MUTATED       1                         1   103
  DEL PEAK 29(16Q12.1) WILD-TYPE     4                         0   223
D51V13, multiclass
                           clus
vv                          DEL PEAK 29(16Q12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              103
                           clus
vv                          DEL PEAK 29(16Q12.1) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  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"
D51V14, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q12.1) MUTATED     3 106
  DEL PEAK 29(16Q12.1) WILD-TYPE   4 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q12.1) MUTATED      3  106
  DEL PEAK 29(16Q12.1) WILD-TYPE    4  228
                        clus
vv                       DEL PEAK 29(16Q12.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          106
                        clus
vv                       DEL PEAK 29(16Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            228
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 30(16Q24.3) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(16Q24.3) MUTATED    57  62
  DEL PEAK 30(16Q24.3) WILD-TYPE 111 103
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                           119                            214 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                            62                            103 
$`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        86.76        44.19        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        21.44 
TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM 
       47.87        22.06        10.22         4.18       142.45        75.65 
TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 
       24.07        21.93        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        23.15         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        36.85        39.62        12.03        32.15         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        55.69         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       125.65 
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        21.73        33.60        31.40 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19T 
       12.95        25.18        11.11        42.84         9.57         6.58 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1Z0 
       17.72         1.87         1.71         3.58         2.20        23.80 
TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU 
        3.39        11.08        12.92        52.08        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FW-A3R5 TCGA-FW-A3TU 
       27.39         0.82         3.22         7.36         0.99         0.13 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        7.23         0.85        44.28        16.24        15.42        14.70 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        14.50         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-A8ZX 
        0.33        11.84         5.49         6.48         3.72        21.83 
TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94         6.18         4.70         6.67         5.98 

$`DEL PEAK 30(16Q24.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       28.08        81.24        85.32         8.38        21.14        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
        7.50        36.16         6.31        59.57        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32        82.29        24.00         6.31         9.34       103.59 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78       110.24        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       23.11        29.72        15.19       108.79        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 
       87.62        11.44         5.56         4.01         5.72         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-A5UL 
        7.00        17.56        13.15         0.13        19.00        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 
       13.22         0.20        11.57        10.55         1.35         5.13 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       60.23        15.85         9.21         7.99        37.97        62.79 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        8.55         1.08         9.50         8.09         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       30.44         2.43        49.22        36.30        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       28.31        33.83         1.15        13.02        34.98        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
       98.27         2.70         6.18        47.51        29.46         2.73 
TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
        7.96       111.91        25.08        26.99        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH 
       52.67       124.31        51.62         3.68        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
        3.22        21.60        16.14         0.95        27.35        18.41 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       18.61        38.40         5.72        76.41         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       34.68        36.07        78.44        11.80         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       12.62        11.74         9.04         6.58        22.49         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA 
       18.41        85.74        15.72         6.71         5.36        13.28 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
        4.70         3.29        64.47         3.45        11.01        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         7.30        20.38         8.22        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        30.87        12.89        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.15         5.23        53.85        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
        5.98         6.41         2.27         0.20         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
        9.90        11.61        31.33        84.72        10.13        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A694 TCGA-W3-A824 
       11.84        10.65        14.50        15.81         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        8.98        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
        7.10        18.67        21.07        13.12         3.42         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT 
        1.08        19.96        12.07         8.22 

  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                        142.45                         185.16 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                         14.50                          15.62 
[1] "0.1 - 142.4 (14.5)" "0.1 - 185.2 (15.6)"
[1] "hr=" "1.1"
D52V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(16Q24.3) MUTATED    60  62
  DEL PEAK 30(16Q24.3) WILD-TYPE 113 104
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                           122                            217 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                            62                            104 
$`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        86.76        62.07       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        22.62 
TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM 
      137.92        79.59        11.61        58.52       228.99        95.24 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6EA 
      117.17       151.53        54.67         3.65        22.29        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 
       68.25         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        64.64        56.84 
TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC 
       56.42       195.02        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       126.81        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       158.63       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 
      109.58       148.08        31.40        13.94        98.40        26.37 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A3PL 
       44.05        50.89         8.88       148.18        23.34        33.21 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZJ 
       15.16        34.82       202.65        48.85        15.45        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 
       74.73        53.16        26.56        49.48        27.09        50.14 
TCGA-FS-A4F4 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       66.67        22.92        47.54         7.23         2.04       139.89 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB 
       64.44        62.79        39.58        50.10        21.37       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-WE-A8JZ TCGA-WE-A8K1 
      294.77         6.67        18.05         0.33        24.03        38.56 
TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
       54.38        52.34        22.68        10.36        36.03        14.43 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

$`DEL PEAK 30(16Q24.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       28.08        95.74       103.10        65.49        23.77        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
      113.52        42.08        12.10        59.57        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32       166.52        24.53        13.87         9.34       103.59 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       125.79       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
      125.19        30.84        15.19       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      137.79        29.06       129.63         6.41        18.12        11.34 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       11.11         9.90        22.95        48.89       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      194.83       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH 
       68.09        28.60        10.49       215.44        13.87        17.85 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       27.22        14.70        68.15       133.81        91.56       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N 
       63.35        47.84        63.78        72.07         2.60        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 
       37.35        14.47        55.92       369.93        25.87       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       36.82        86.14        59.28       314.56       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       89.33        54.74        79.66        75.48        90.97        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-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MN 
       61.51       103.27       268.73        16.96       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      248.65       134.40       162.48        71.21       124.31        51.62 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
        3.68        23.47       138.81       172.18        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
      201.80        27.35        51.35        35.44        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       77.75        48.89        12.59        13.02       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A1A1 
        6.44       131.51        61.05       162.08        37.25        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-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
      210.08         7.00        38.27        29.46        94.39       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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
      357.37        53.52        40.27         9.70        32.75        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 
      101.26       133.55        11.41       148.80        27.02        77.82 
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-A6C9 TCGA-GN-A264 
        0.20         0.16        19.30         9.90        11.74       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A9SD 
       84.72        10.13        32.48        46.36        12.62        59.41 
TCGA-HR-A2OH TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
       65.88         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       42.08       219.16       105.04         8.61        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       59.41         3.75        43.73         2.20        30.18        15.16 
TCGA-Z2-A8RT 
       23.64 

  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                          0.33                           0.16 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                        357.04                         369.93 
  DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE 
                        51.615                         48.890 
[1] "0.3 - 357.0 (51.6)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.1"
D52V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 30(16Q24.3) MUTATED                   24             3
  DEL PEAK 30(16Q24.3) WILD-TYPE                 37             2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 30(16Q24.3) MUTATED                                          20
  DEL PEAK 30(16Q24.3) WILD-TYPE                                        52
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 30(16Q24.3) MUTATED                    77
  DEL PEAK 30(16Q24.3) WILD-TYPE                 132
D52V4, multiclass
                                           clus
vv                                          DEL PEAK 30(16Q24.3) MUTATED
  DISTANT METASTASIS                                                  24
  PRIMARY TUMOR                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           20
  REGIONAL LYMPH NODE                                                 77
                                           clus
vv                                          DEL PEAK 30(16Q24.3) WILD-TYPE
  DISTANT METASTASIS                                                    37
  PRIMARY TUMOR                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             52
  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 30(16Q24.3) MUTATED             3       4       7        8        8
  DEL PEAK 30(16Q24.3) WILD-TYPE           9       3      21        9       19
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 30(16Q24.3) MUTATED          8         3        13         7
  DEL PEAK 30(16Q24.3) WILD-TYPE       14        11         6         5
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 30(16Q24.3) MUTATED          10          5         11         17
  DEL PEAK 30(16Q24.3) WILD-TYPE        25         10         21         41
                                vv
clus                             STAGE IV
  DEL PEAK 30(16Q24.3) MUTATED          7
  DEL PEAK 30(16Q24.3) WILD-TYPE       12
D52V5, multiclass
             clus
vv            DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  I OR II NOS                            3                              9
  STAGE 0                                4                              3
  STAGE I                                7                             21
  STAGE IA                               8                              9
  STAGE IB                               8                             19
  STAGE II                               8                             14
  STAGE IIA                              3                             11
  STAGE IIB                             13                              6
  STAGE IIC                              7                              5
  STAGE III                             10                             25
  STAGE IIIA                             5                             10
  STAGE IIIB                            11                             21
  STAGE IIIC                            17                             41
  STAGE IV                               7                             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
  DEL PEAK 30(16Q24.3) MUTATED      22 20 26 28
  DEL PEAK 30(16Q24.3) WILD-TYPE    41 51 48 39
D52V6, multiclass
       clus
vv      DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  T0+T1                           22                             41
  T2                              20                             51
  T3                              26                             48
  T4                              28                             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 30(16Q24.3) MUTATED    66  18  12  16
  DEL PEAK 30(16Q24.3) WILD-TYPE 102  43  26  31
D52V7, multiclass
    clus
vv   DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  N0                           66                            102
  N1                           18                             43
  N2                           12                             26
  N3                           16                             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 30(16Q24.3) MUTATED   108   0   2   1   5
  DEL PEAK 30(16Q24.3) WILD-TYPE 198   4   1   3   4
D52V8, multiclass
     clus
vv    DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  M0                           108                            198
  M1                             0                              4
  M1A                            2                              1
  M1B                            1                              3
  M1C                            5                              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"
D52V9, binary
                                cls
clus                              0  1
  DEL PEAK 30(16Q24.3) MUTATED   49 33
  DEL PEAK 30(16Q24.3) WILD-TYPE 80 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.3) MUTATED     49   33
  DEL PEAK 30(16Q24.3) WILD-TYPE   80   54
     clus
vv    DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  NO                            49                             80
  YES                           33                             54
[1] 2 2
[1] FALSE
D52V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q24.3) MUTATED    14 111
  DEL PEAK 30(16Q24.3) WILD-TYPE  29 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.3) MUTATED     14  111
  DEL PEAK 30(16Q24.3) WILD-TYPE   29  193
     clus
vv    DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  NO                            14                             29
  YES                          111                            193
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q24.3) MUTATED    50  75
  DEL PEAK 30(16Q24.3) WILD-TYPE  81 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.3) MUTATED     50   75
  DEL PEAK 30(16Q24.3) WILD-TYPE   81  142
        clus
vv       DEL PEAK 30(16Q24.3) MUTATED DEL PEAK 30(16Q24.3) WILD-TYPE
  FEMALE                           50                             81
  MALE                             75                            142
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(16Q24.3) MUTATED       1                         1   117
  DEL PEAK 30(16Q24.3) WILD-TYPE     4                         0   209
D52V13, multiclass
                           clus
vv                          DEL PEAK 30(16Q24.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              117
                           clus
vv                          DEL PEAK 30(16Q24.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                209
[1] 3 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 30(16Q24.3) MUTATED     3 120
  DEL PEAK 30(16Q24.3) WILD-TYPE   4 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.3) MUTATED      3  120
  DEL PEAK 30(16Q24.3) WILD-TYPE    4  214
                        clus
vv                       DEL PEAK 30(16Q24.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       DEL PEAK 30(16Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            214
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 31(17P13.3) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(17P13.3) MUTATED    61  64
  DEL PEAK 31(17P13.3) WILD-TYPE 107 101
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                           125                            208 
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                            64                            101 
$`DEL PEAK 31(17P13.3) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
        3.02         6.97         6.97        22.55        45.83        10.29 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN 
       88.50        68.22        11.41         7.50        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB 
       64.44         6.31        21.44        25.78        47.87        29.72 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       22.06         4.18        38.93        75.65       124.47        87.62 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I5 
        9.90        11.31        48.79        35.80        51.12        44.52 
TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN 
       25.15         7.00        17.56         0.20        13.35        13.22 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C 
       11.57         8.12         5.13         4.31         4.34        37.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       62.79         8.55        36.85         1.08        39.62         9.50 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99        30.44         2.43         8.09        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 
        9.67        34.29        30.08         5.42        34.98         8.84 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MP 
       98.27        47.51         9.53        44.25        56.02        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       21.60        60.49        53.16         5.56       124.31        51.62 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       30.15        21.60        21.60        16.14         0.95        21.73 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19S 
       31.40        18.61         5.72         3.78        11.11        36.07 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
        1.51        12.62        22.49        18.41        85.74         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 
        3.58         5.36         2.20        64.47         3.45        15.52 
TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       30.87        52.08         8.65        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 
        0.82         3.22        28.73        10.78         0.99        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-QB-AA9O 
       10.13        16.24        15.42        10.65        14.50        18.05 
TCGA-RP-A694 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-A8ZY 
        0.69        71.01        11.84         5.49         3.42         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3V 
        1.08        19.96         1.94         6.18         5.98 

$`DEL PEAK 31(17P13.3) 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-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JC 
       28.08        81.24        85.32         8.38        21.14        86.76 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       44.19        36.16         6.31        59.57       114.67        15.25 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       31.30        54.31        32.28        32.61       110.24        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       13.68        17.72        23.11        10.22        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      108.79        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        5.72        13.22        14.60        10.03        39.19        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-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 
       14.83        13.15         0.13        23.15        19.00         0.20 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B 
       10.55         6.31         1.12         1.35        12.20        60.23 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       15.85         9.21         1.18         7.99         9.90        11.15 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 
       12.03         8.09         8.84        32.15        11.31        36.33 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       51.12        17.98        60.00        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83        55.69         1.15        13.02 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
       36.33         2.70         6.18        29.46         2.73         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MT 
       14.56        63.42       125.65       111.91        25.08        52.67 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73         3.68        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 
       22.92        22.22        27.35        18.41        33.60        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
       38.40        76.41        25.18         3.52        11.90       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K 
       13.08        11.74         9.04         6.58         1.71         5.62 
TCGA-FR-A69P TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 
       15.72        13.28         4.70         3.29        11.01        23.80 
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-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-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        8.81        49.15         5.23        53.85         7.36        14.20 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD 
       31.33        12.16        14.70        11.84        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 
       15.81         0.43        11.05         5.79         0.33       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K5 
        8.98        60.03         2.99        10.98       185.16         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX 
        7.10        18.67        21.07        13.12         3.72        21.83 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       12.07         4.70         8.22         6.67 

  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                          0.20                           0.13 
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                        124.47                         185.16 
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                         16.24                          14.50 
[1] "0.2 - 124.5 (16.2)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1"  
D53V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(17P13.3) MUTATED    63  64
  DEL PEAK 31(17P13.3) WILD-TYPE 110 102
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                           127                            212 
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                            64                            102 
$`DEL PEAK 31(17P13.3) MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 
       17.03        61.02        12.99        31.59        90.90        43.43 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN 
      115.53       168.00        11.87       113.52       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB 
       66.08        13.87        22.62        26.89       137.92        30.84 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       79.59        58.52        89.13        95.24       161.00       137.79 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
      151.53         3.65         9.90        25.18        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R 
      117.21       107.34        53.92        10.49       215.44        10.16 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 
       17.29        52.01        29.82        94.98        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
      151.27        47.84        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
       56.84        18.61        55.92       369.93        25.87        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GP 
      102.90        36.82        39.29        67.43        48.72        13.91 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG 
       44.88        21.67       129.27        61.51        47.28       103.20 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
      167.90       248.65        43.23       134.40       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      124.31        51.62        54.51        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19C 
      201.80       109.58        31.40        35.44         9.17        48.89 
TCGA-ER-A19F TCGA-ER-A19S TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN 
       26.37        37.25        20.15        31.27        46.98        92.98 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YW 
      174.21       210.08        15.16         7.00        34.82       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       48.59        28.08        32.75        74.73       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 
       26.56        49.48        27.09        50.14        28.73        12.43 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
       22.92        84.72        10.13        64.44        62.79        12.62 
TCGA-GN-A8LL TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       21.37        18.05         0.69       105.04        24.03        38.56 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
        3.75        43.73         2.20        30.18        10.36        36.03 
TCGA-Z2-AA3V 
       11.74 

$`DEL PEAK 31(17P13.3) 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-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JC 
       28.08        95.74       103.10        65.49        23.77        86.76 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       62.07        42.08        12.10        59.57       130.72        58.06 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       56.35       145.12        32.94        63.81       125.79       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      178.32        18.18       125.19        11.61        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX 
      170.20        29.06       129.63       117.17        54.67         6.41 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG 
       18.12        11.34        22.29        11.11        66.25        22.95 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
       20.38       194.83       176.55        35.93        61.18        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       23.44        68.09        28.60        15.68        13.87        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
       68.25        54.02         6.35        12.20        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       33.73        14.70        26.89       133.81        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A29Q 
       13.55        63.35        80.61        13.97        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       14.47       195.02        46.82        86.14        59.28       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      161.03       208.04        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       90.97       126.81        14.30        55.59        94.82        28.83 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       19.76       103.27       268.73        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD 
      158.63       203.05        47.54        71.21       122.73         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA 
       13.81        23.47       138.81       172.18       127.20        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        51.35       148.08        13.94        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        12.59        13.02       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T 
      131.51        61.05        44.05       162.08        50.89         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH 
      148.18        79.99        43.82        23.34        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7UA 
      247.04        80.32        33.21         6.77        15.72        38.27 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       29.46        94.39       228.59       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        47.38        23.93       101.26        11.41       148.80 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC 
       27.02        77.82        66.67       174.84        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A26A 
        7.23         2.04        11.74       139.89       117.93        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       39.58        46.36        50.10        59.41        65.88       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
      294.77         6.67         0.33       212.22        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
        4.01        42.08       219.16        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P 
       56.98        59.41        52.34        22.68        15.16        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
       23.64        93.07 

  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                          0.69                           0.16 
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                        369.93                         357.37 
  DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE 
                         47.84                          53.77 
[1] "0.7 - 369.9 (47.8)" "0.2 - 357.4 (53.8)"
[1] "hr=" "1.2"
D53V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 31(17P13.3) MUTATED                   22             2
  DEL PEAK 31(17P13.3) WILD-TYPE                 39             3
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 31(17P13.3) MUTATED                                          19
  DEL PEAK 31(17P13.3) WILD-TYPE                                        53
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 31(17P13.3) MUTATED                    88
  DEL PEAK 31(17P13.3) WILD-TYPE                 121
D53V4, multiclass
                                           clus
vv                                          DEL PEAK 31(17P13.3) MUTATED
  DISTANT METASTASIS                                                  22
  PRIMARY TUMOR                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           19
  REGIONAL LYMPH NODE                                                 88
                                           clus
vv                                          DEL PEAK 31(17P13.3) WILD-TYPE
  DISTANT METASTASIS                                                    39
  PRIMARY TUMOR                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             53
  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
  DEL PEAK 31(17P13.3) MUTATED             6       4      13        9       11
  DEL PEAK 31(17P13.3) WILD-TYPE           6       3      15        8       16
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 31(17P13.3) MUTATED          5         4         7         4
  DEL PEAK 31(17P13.3) WILD-TYPE       17        10        12         8
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 31(17P13.3) MUTATED          11          9         11         22
  DEL PEAK 31(17P13.3) WILD-TYPE        24          6         21         36
                                vv
clus                             STAGE IV
  DEL PEAK 31(17P13.3) MUTATED          5
  DEL PEAK 31(17P13.3) WILD-TYPE       14
D53V5, multiclass
             clus
vv            DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE
  I OR II NOS                            6                              6
  STAGE 0                                4                              3
  STAGE I                               13                             15
  STAGE IA                               9                              8
  STAGE IB                              11                             16
  STAGE II                               5                             17
  STAGE IIA                              4                             10
  STAGE IIB                              7                             12
  STAGE IIC                              4                              8
  STAGE III                             11                             24
  STAGE IIIA                             9                              6
  STAGE IIIB                            11                             21
  STAGE IIIC                            22                             36
  STAGE IV                               5                             14
[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(17P13.3) MUTATED      23 31 26 25
  DEL PEAK 31(17P13.3) WILD-TYPE    40 40 48 42
D53V6, multiclass
       clus
vv      DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE
  T0+T1                           23                             40
  T2                              31                             40
  T3                              26                             48
  T4                              25                             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(17P13.3) MUTATED    62  23  14  19
  DEL PEAK 31(17P13.3) WILD-TYPE 106  38  24  28
D53V7, multiclass
    clus
vv   DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE
  N0                           62                            106
  N1                           23                             38
  N2                           14                             24
  N3                           19                             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 31(17P13.3) MUTATED   120   0   0   2   4
  DEL PEAK 31(17P13.3) WILD-TYPE 186   4   3   2   5
D53V8, multiclass
     clus
vv    DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE
  M0                           120                            186
  M1                             0                              4
  M1A                            0                              3
  M1B                            2                              2
  M1C                            4                              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"
D53V9, binary
                                cls
clus                              0  1
  DEL PEAK 31(17P13.3) MUTATED   55 34
  DEL PEAK 31(17P13.3) WILD-TYPE 74 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17P13.3) MUTATED     55   34
  DEL PEAK 31(17P13.3) WILD-TYPE   74   53
     clus
vv    DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE
  NO                            55                             74
  YES                           34                             53
[1] 2 2
[1] FALSE
D53V10, binary
                                cls
clus                               0   1
  DEL PEAK 31(17P13.3) MUTATED    14 117
  DEL PEAK 31(17P13.3) WILD-TYPE  29 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17P13.3) MUTATED     14  117
  DEL PEAK 31(17P13.3) WILD-TYPE   29  187
     clus
vv    DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE
  NO                            14                             29
  YES                          117                            187
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, binary
                                cls
clus                               0   1
  DEL PEAK 31(17P13.3) MUTATED    41  90
  DEL PEAK 31(17P13.3) WILD-TYPE  90 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17P13.3) MUTATED     41   90
  DEL PEAK 31(17P13.3) WILD-TYPE   90  127
        clus
vv       DEL PEAK 31(17P13.3) MUTATED DEL PEAK 31(17P13.3) WILD-TYPE
  FEMALE                           41                             90
  MALE                             90                            127
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(17P13.3) MUTATED       1                         1   121
  DEL PEAK 31(17P13.3) WILD-TYPE     4                         0   205
D53V13, multiclass
                           clus
vv                          DEL PEAK 31(17P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                              121
                           clus
vv                          DEL PEAK 31(17P13.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              0
  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"
D53V14, binary
                                cls
clus                               0   1
  DEL PEAK 31(17P13.3) MUTATED     1 127
  DEL PEAK 31(17P13.3) WILD-TYPE   6 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17P13.3) MUTATED      1  127
  DEL PEAK 31(17P13.3) WILD-TYPE    6  207
                        clus
vv                       DEL PEAK 31(17P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          127
                        clus
vv                       DEL PEAK 31(17P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            207
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 32(19P13.3) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(19P13.3) MUTATED    45  50
  DEL PEAK 32(19P13.3) WILD-TYPE 123 115
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            95                            238 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            50                            115 
$`DEL PEAK 32(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-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI 
       25.78       110.24        52.01        29.72        10.22         4.18 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z3 
       75.65       124.47        87.62         5.56        24.07        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 
        5.72        11.31        48.79        35.80        10.03        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44R 
       36.69        25.15         4.93         6.64        17.56         0.20 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A20I 
       19.00        13.35        11.57         4.31         9.21         1.18 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29V 
       37.97        11.15         8.55        36.85         9.50         2.43 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GS 
        8.09        11.31        36.33        51.12        28.31        13.02 
TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       36.33        44.25        26.99        21.60        53.16        52.67 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA 
      122.73        51.62         3.68        22.92        21.60        22.22 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19M 
       27.35        31.40        25.18         3.78        34.88        28.60 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV 
        9.57        17.72         1.87        12.62        11.74        22.49 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
       18.41        85.74        15.72         8.22        11.08        30.87 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TU 
        8.65        40.64        27.39         5.98         2.27         0.13 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A8LL TCGA-W3-AA1V 
        0.16         7.23        44.28        15.42        14.50        10.98 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-YG-AA3P TCGA-Z2-AA3V 
       11.84         5.49        18.67         4.70         5.98 

$`DEL PEAK 32(19P13.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2J8 
       70.16       110.79        28.08        45.83        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        88.50        68.22        86.76        44.19         7.50 
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        59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC 
       32.61        47.87        13.68        17.72        23.11        22.06 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D9-A3Z1 
       15.19       142.45       108.79        38.93        11.44         4.01 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        13.22        14.60        51.12        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
        9.99        22.36        19.36         7.00        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
        0.13        23.15        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-A20B 
        8.12         1.12         1.35        12.20         5.13        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29L 
        4.34        15.85         7.99         9.90        62.79         1.08 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       39.62        12.03         8.09         8.84         9.99        30.44 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD 
       32.15        49.22        36.30         9.67        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 
       33.83        55.69         5.42         1.15        34.98         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73         7.96        14.56        63.42       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
       56.02        25.08        60.49         5.56       124.31        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        15.95        12.72         3.22        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        0.95        18.41        21.73        33.60        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       38.40         5.72        76.41         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
      114.15         4.21        13.45        42.84        34.68        36.07 
TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
        6.58        78.44        11.80         1.51        13.08         9.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
        6.58         1.71         5.62         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       13.28         2.20         4.70         3.29        64.47         3.45 
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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        3.39        20.38        19.53         7.17        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       47.38        52.08         8.81        49.15         8.68         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        5.23        53.85         3.22         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT 
       10.78         6.41         0.20         0.99        17.33         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.85        11.61        31.33        84.72        10.13        16.24 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       15.81         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       164.19         8.98        60.03         2.99       185.16 
TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       71.01         6.48         7.10        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        3.42        21.83         5.36         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       12.07         6.18         8.22         6.67 

  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                          0.13                           0.13 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                        124.47                         185.16 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                         17.72                          14.37 
[1] "0.1 - 124.5 (17.7)" "0.1 - 185.2 (14.4)"
[1] "hr=" "1.1"
D54V2, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(19P13.3) MUTATED    47  50
  DEL PEAK 32(19P13.3) WILD-TYPE 126 116
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            97                            242 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            50                            116 
$`DEL PEAK 32(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-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI 
       26.89       125.79       135.75        30.84        11.61        58.52 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       95.24       161.00       137.79       129.63       117.17       151.53 
TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       18.12        22.29        11.11        25.18        48.89        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       20.38       107.34        61.18        53.92        65.92        68.09 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A185 
      215.44        10.16        54.02        17.29        29.82         4.96 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
      168.26        13.55        47.84        13.97        72.07        64.64 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB 
       18.61        25.87        17.92        46.82        86.14        59.28 
TCGA-EE-A2GM TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MQ 
       75.48        55.59        94.82       103.20       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J4 
      162.48        71.21       122.73        51.62         3.68       127.20 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19C 
       36.95        53.19        27.35        31.40        98.40        48.89 
TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG 
      152.35        61.05        50.89       148.18        23.34        31.27 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZD 
       32.05        46.98        92.98       174.21        15.72        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FB 
       15.45        32.75       133.55        53.16        49.48        26.73 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 
       77.88        47.54         0.16         7.23       139.89        62.79 
TCGA-GN-A8LL TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-YG-AA3P 
       21.37        42.08        24.03        38.56        90.28        14.43 
TCGA-Z2-AA3V 
       11.74 

$`DEL PEAK 32(19P13.3) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2J8 
       71.80       133.25        28.08        90.90       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       115.53       168.00        86.76        62.07       113.52 
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        59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC 
       63.81       137.92       178.32        18.18       125.19        79.59 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D9-A149 
       15.19       228.99       170.20        89.13        29.06        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-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 
      117.21       194.83       176.55        35.93        23.44        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN 
       10.49        15.68        13.87        17.85        68.25        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        6.35        12.20        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89        68.15       133.81       151.27        91.56 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       63.35        80.61        63.78         2.60        56.84        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       37.35        14.47        55.92       369.93       195.02       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.82        39.29        67.43       314.56       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        89.33        54.74        79.66        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        14.30        44.88        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       268.73        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      134.40        53.26       124.31        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE 
      138.81       172.18        64.08        34.32       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      109.58       148.08        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
       77.75        12.59        13.02        26.37       268.93         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 
      131.51        44.05       162.08        37.25         8.88        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-ER-A42K TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
        6.77       210.08        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       29.46        94.39       216.92        48.59       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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       40.27         9.70        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       11.41       148.80        26.56        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC 
       50.14        66.67        28.73       174.84        12.43        49.45 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.20        22.92        19.30         9.90         2.04        11.74 
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-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       46.36        12.62        50.10        59.41        65.88       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      294.77         6.67        18.05         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 
       63.02       121.08         4.01       219.16       105.04        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
        8.61        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        15.16        36.03 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
       23.64        93.07 

  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                          0.16                           0.20 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                        248.65                         369.93 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                         49.48                          50.45 
[1] "0.2 - 248.7 (49.5)" "0.2 - 369.9 (50.5)"
[1] "hr=" "1.2"
D54V3, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 32(19P13.3) MUTATED                   16             1
  DEL PEAK 32(19P13.3) WILD-TYPE                 45             4
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 32(19P13.3) MUTATED                                          17
  DEL PEAK 32(19P13.3) WILD-TYPE                                        55
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 32(19P13.3) MUTATED                    64
  DEL PEAK 32(19P13.3) WILD-TYPE                 145
D54V4, multiclass
                                           clus
vv                                          DEL PEAK 32(19P13.3) MUTATED
  DISTANT METASTASIS                                                  16
  PRIMARY TUMOR                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                           17
  REGIONAL LYMPH NODE                                                 64
                                           clus
vv                                          DEL PEAK 32(19P13.3) WILD-TYPE
  DISTANT METASTASIS                                                    45
  PRIMARY TUMOR                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                             55
  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
  DEL PEAK 32(19P13.3) MUTATED             5       1       6        6        8
  DEL PEAK 32(19P13.3) WILD-TYPE           7       6      22       11       19
                                vv
clus                             STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 32(19P13.3) MUTATED          4         2         5         3
  DEL PEAK 32(19P13.3) WILD-TYPE       18        12        14         9
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 32(19P13.3) MUTATED          13          2         13         18
  DEL PEAK 32(19P13.3) WILD-TYPE        22         13         19         40
                                vv
clus                             STAGE IV
  DEL PEAK 32(19P13.3) MUTATED          4
  DEL PEAK 32(19P13.3) WILD-TYPE       15
D54V5, multiclass
             clus
vv            DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  I OR II NOS                            5                              7
  STAGE 0                                1                              6
  STAGE I                                6                             22
  STAGE IA                               6                             11
  STAGE IB                               8                             19
  STAGE II                               4                             18
  STAGE IIA                              2                             12
  STAGE IIB                              5                             14
  STAGE IIC                              3                              9
  STAGE III                             13                             22
  STAGE IIIA                             2                             13
  STAGE IIIB                            13                             19
  STAGE IIIC                            18                             40
  STAGE IV                               4                             15
[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 32(19P13.3) MUTATED      21 21 18 20
  DEL PEAK 32(19P13.3) WILD-TYPE    42 50 56 47
D54V6, multiclass
       clus
vv      DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  T0+T1                           21                             42
  T2                              21                             50
  T3                              18                             56
  T4                              20                             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 32(19P13.3) MUTATED    45  18  15  15
  DEL PEAK 32(19P13.3) WILD-TYPE 123  43  23  32
D54V7, multiclass
    clus
vv   DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  N0                           45                            123
  N1                           18                             43
  N2                           15                             23
  N3                           15                             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 32(19P13.3) MUTATED    88   0   1   1   3
  DEL PEAK 32(19P13.3) WILD-TYPE 218   4   2   3   6
D54V8, multiclass
     clus
vv    DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  M0                            88                            218
  M1                             0                              4
  M1A                            1                              2
  M1B                            1                              3
  M1C                            3                              6
[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 32(19P13.3) MUTATED   38 25
  DEL PEAK 32(19P13.3) WILD-TYPE 91 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED     38   25
  DEL PEAK 32(19P13.3) WILD-TYPE   91   62
     clus
vv    DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  NO                            38                             91
  YES                           25                             62
[1] 2 2
[1] FALSE
D54V10, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.3) MUTATED    10  88
  DEL PEAK 32(19P13.3) WILD-TYPE  33 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED     10   88
  DEL PEAK 32(19P13.3) WILD-TYPE   33  216
     clus
vv    DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  NO                            10                             33
  YES                           88                            216
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.3) MUTATED    42  56
  DEL PEAK 32(19P13.3) WILD-TYPE  89 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED     42   56
  DEL PEAK 32(19P13.3) WILD-TYPE   89  161
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  FEMALE                           42                             89
  MALE                             56                            161
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(19P13.3) MUTATED       1                         0    94
  DEL PEAK 32(19P13.3) WILD-TYPE     4                         1   232
D54V13, multiclass
                           clus
vv                          DEL PEAK 32(19P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               94
                           clus
vv                          DEL PEAK 32(19P13.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                232
[1] 3 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 32(19P13.3) MUTATED     1  95
  DEL PEAK 32(19P13.3) WILD-TYPE   6 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED      1   95
  DEL PEAK 32(19P13.3) WILD-TYPE    6  239
                        clus
vv                       DEL PEAK 32(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           95
                        clus
vv                       DEL PEAK 32(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            239
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 33(XP21.1) MUTATION ANALYSIS
D55V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 33(XP21.1) MUTATED    39  41
  DEL PEAK 33(XP21.1) WILD-TYPE 129 124
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                           80                           253 
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                           41                           124 
$`DEL PEAK 33(XP21.1) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JL 
      111.09        32.42        28.08        10.29         7.50        92.42 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       15.25        46.98        61.38        21.44        25.78       110.24 
TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       47.87        22.06        87.62         5.56        21.93         5.72 
TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       35.80        44.52        25.15         4.31         4.34        15.85 
TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 
        1.18        11.15         8.09         2.43         8.09        36.30 
TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS 
       34.29         1.15         2.73       125.65        56.02        53.16 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 
        3.68        13.81        12.72        16.14        21.73        31.40 
TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-FR-A7U8 
       13.45         1.87         1.51        13.08        11.74         3.58 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       64.47        11.01        14.24        11.08         7.17        30.87 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.65         8.81        49.15         5.23        53.85         7.36 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C8 TCGA-GF-A6C9 
       10.78         5.98         0.13         0.16         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1V 
       44.28        15.42        14.50         0.43        11.05        10.98 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3P 
       11.84        18.67         3.42         5.36         1.08         4.70 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
        8.22         6.67 

$`DEL PEAK 33(XP21.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      110.79        22.55        45.83        81.24        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        86.76        11.41        44.19 
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        59.57       114.67 
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-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       54.31        32.28        32.61        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       23.11        29.72        10.22        15.19         4.18       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GS 
      108.79        38.93        75.65       124.47        11.44        24.07 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01         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-A1I7 
       51.12        10.03        39.19        13.68         9.99        36.69 
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-A5SH 
       14.83        13.15         0.20         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
        8.12         1.12         1.35        12.20         5.13        60.23 
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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       36.85         1.08        39.62         9.50        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        9.99        30.44        32.15        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.33        51.12        17.98        60.00        47.21        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        55.69 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        5.42        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-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
        7.96        14.56        63.42       111.91        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        60.49        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       51.62        30.15        15.95         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       21.60        22.22         0.95        27.35        18.41        33.60 
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-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-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES 
        6.58        17.72        78.44        11.80        12.62         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72         6.71         5.36        13.28         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.29         3.45        23.80        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        3.39        20.38         8.22        19.53        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       47.38        52.08        40.64         8.68        27.39         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
        3.22        28.73        14.20         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        17.33         9.90         7.23        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        16.24        12.16        14.70        11.84        10.65 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       14.50        14.50        15.81         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       164.19         8.98        60.03         2.99       185.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       71.01         5.49         6.48         7.10        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        3.72        21.83        19.96         1.94        12.07         6.18 
TCGA-Z2-AA3V 
        5.98 

  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                         0.13                          0.13 
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                       125.65                        185.16 
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                        11.79                         16.01 
[1] "0.1 - 125.7 (11.8)" "0.1 - 185.2 (16.0)"
[1] "hr=" "1.3"
D55V2, survival
                               sevent
clus2                             0   1
  DEL PEAK 33(XP21.1) MUTATED    41  41
  DEL PEAK 33(XP21.1) WILD-TYPE 132 125
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                           82                           257 
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                           41                           125 
$`DEL PEAK 33(XP21.1) MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JL 
      112.04       112.57        28.08        43.43       113.52       171.58 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       58.06        46.98        86.93        22.62        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1X3 
      137.92        79.59       137.79       129.63       151.53        18.12 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A185 
       22.29        11.11        36.03       107.34        53.92         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29Q TCGA-EE-A29V 
      151.27        91.56        13.55        13.97        37.35        25.87 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2MK 
       17.92        36.82        67.43        14.30       268.73       158.63 
TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 
      167.90       162.48         3.68        13.81       138.81        34.32 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      109.58        31.40       131.51        23.34        20.15        16.37 
TCGA-ER-A2NH TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZF 
       32.05        15.16       216.92       228.59        20.91        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ 
        9.70        32.75       133.55        11.41       148.80        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-FW-A3TV 
       77.82        66.67        12.43        26.73        47.54         0.16 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A8LK TCGA-LH-A9QB 
        2.04        11.74       139.89        62.79        50.10       357.04 
TCGA-OD-A75X TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZT TCGA-WE-A8ZY 
      294.77        42.08        24.03        90.28         3.75        43.73 
TCGA-WE-AA9Y TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        2.20        14.43        23.64        93.07 

$`DEL PEAK 33(XP21.1) WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        31.59        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        86.76        11.87        62.07 
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        59.57       130.72 
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-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
      145.12        32.94        63.81       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
      125.19        30.84        11.61        15.19        58.52       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GS 
      170.20        89.13        95.24       161.00        29.06       117.17 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
       54.67         3.65         6.41        11.34         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-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-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-A5UN TCGA-EB-A5VV 
       17.85        68.25        54.02        17.29        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       12.20        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       14.70        26.89        68.15       133.81       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        56.42        14.47        55.92       369.93 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02        46.82       102.90        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       79.66        75.48        90.97       126.81        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-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       203.05        47.54       248.65        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       71.21        53.26       124.31       122.73        51.62        54.51 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
       23.47       172.18       127.20        36.95        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      201.80        27.35        51.35       148.08        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-A19M 
       13.02        26.37       268.93       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       79.99        43.82        31.27       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       210.08 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX 
        7.00        38.27        34.82        29.46        94.39        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       53.52        40.27        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
       53.16        26.56        49.48        27.09        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A5DY 
      174.84        49.45        77.88         0.20        22.92        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        9.90         7.23       117.93        84.72        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       32.48        39.58        46.36        12.62        21.37        59.41 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       65.88         6.67        18.05         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       63.02       121.08         4.01       219.16       105.04        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       54.38         8.61        56.98        59.41        52.34        22.68 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3V 
       30.18        10.36        15.16        36.03        11.74 

  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                         0.16                          0.20 
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                       357.04                        369.93 
  DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE 
                       42.755                        52.010 
[1] "0.2 - 357.0 (42.8)" "0.2 - 369.9 (52.0)"
[1] "hr=" "1"  
D55V3, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 33(XP21.1) MUTATED                   21             1
  DEL PEAK 33(XP21.1) WILD-TYPE                 40             4
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  DEL PEAK 33(XP21.1) MUTATED                                          14
  DEL PEAK 33(XP21.1) WILD-TYPE                                        58
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 33(XP21.1) MUTATED                    48
  DEL PEAK 33(XP21.1) WILD-TYPE                 161
D55V4, multiclass
                                           clus
vv                                          DEL PEAK 33(XP21.1) MUTATED
  DISTANT METASTASIS                                                 21
  PRIMARY TUMOR                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                          14
  REGIONAL LYMPH NODE                                                48
                                           clus
vv                                          DEL PEAK 33(XP21.1) WILD-TYPE
  DISTANT METASTASIS                                                   40
  PRIMARY TUMOR                                                         4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                            58
  REGIONAL LYMPH NODE                                                 161
[1] 4 2
[1] 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 33(XP21.1) MUTATED             4       3       4        1        6
  DEL PEAK 33(XP21.1) WILD-TYPE           8       4      24       16       21
                               vv
clus                            STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 33(XP21.1) MUTATED          6         3        10         2
  DEL PEAK 33(XP21.1) WILD-TYPE       16        11         9        10
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 33(XP21.1) MUTATED           6          2          5         17
  DEL PEAK 33(XP21.1) WILD-TYPE        29         13         27         41
                               vv
clus                            STAGE IV
  DEL PEAK 33(XP21.1) MUTATED          8
  DEL PEAK 33(XP21.1) WILD-TYPE       11
D55V5, multiclass
             clus
vv            DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE
  I OR II NOS                           4                             8
  STAGE 0                               3                             4
  STAGE I                               4                            24
  STAGE IA                              1                            16
  STAGE IB                              6                            21
  STAGE II                              6                            16
  STAGE IIA                             3                            11
  STAGE IIB                            10                             9
  STAGE IIC                             2                            10
  STAGE III                             6                            29
  STAGE IIIA                            2                            13
  STAGE IIIB                            5                            27
  STAGE IIIC                           17                            41
  STAGE IV                              8                            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 33(XP21.1) MUTATED      13 13 19 19
  DEL PEAK 33(XP21.1) WILD-TYPE    50 58 55 48
D55V6, multiclass
       clus
vv      DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE
  T0+T1                          13                            50
  T2                             13                            58
  T3                             19                            55
  T4                             19                            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 33(XP21.1) MUTATED    40  16   5  13
  DEL PEAK 33(XP21.1) WILD-TYPE 128  45  33  34
D55V7, multiclass
    clus
vv   DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE
  N0                          40                           128
  N1                          16                            45
  N2                           5                            33
  N3                          13                            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 33(XP21.1) MUTATED    68   1   0   3   5
  DEL PEAK 33(XP21.1) WILD-TYPE 238   3   3   1   4
D55V8, multiclass
     clus
vv    DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE
  M0                           68                           238
  M1                            1                             3
  M1A                           0                             3
  M1B                           3                             1
  M1C                           5                             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"
D55V9, binary
                               cls
clus                              0   1
  DEL PEAK 33(XP21.1) MUTATED    25  24
  DEL PEAK 33(XP21.1) WILD-TYPE 104  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP21.1) MUTATED     25   24
  DEL PEAK 33(XP21.1) WILD-TYPE  104   63
     clus
vv    DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE
  NO                           25                           104
  YES                          24                            63
[1] 2 2
[1] FALSE
D55V10, binary
                               cls
clus                              0   1
  DEL PEAK 33(XP21.1) MUTATED     9  75
  DEL PEAK 33(XP21.1) WILD-TYPE  34 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP21.1) MUTATED      9   75
  DEL PEAK 33(XP21.1) WILD-TYPE   34  229
     clus
vv    DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE
  NO                            9                            34
  YES                          75                           229
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, binary
                               cls
clus                              0   1
  DEL PEAK 33(XP21.1) MUTATED    38  46
  DEL PEAK 33(XP21.1) WILD-TYPE  93 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP21.1) MUTATED     38   46
  DEL PEAK 33(XP21.1) WILD-TYPE   93  171
        clus
vv       DEL PEAK 33(XP21.1) MUTATED DEL PEAK 33(XP21.1) WILD-TYPE
  FEMALE                          38                            93
  MALE                            46                           171
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(XP21.1) MUTATED       0                         0    78
  DEL PEAK 33(XP21.1) WILD-TYPE     5                         1   248
D55V13, multiclass
                           clus
vv                          DEL PEAK 33(XP21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              78
                           clus
vv                          DEL PEAK 33(XP21.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                               248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                               cls
clus                              0   1
  DEL PEAK 33(XP21.1) MUTATED     2  80
  DEL PEAK 33(XP21.1) WILD-TYPE   5 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XP21.1) MUTATED      2   80
  DEL PEAK 33(XP21.1) WILD-TYPE    5  254
                        clus
vv                       DEL PEAK 33(XP21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          80
                        clus
vv                       DEL PEAK 33(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           254
[1] 2 2
[1] FALSE
