[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"        "-oTLIHC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/11541458/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/11548745/transformed.cor.cli.txt"

nPatients in clinical file=317, in cluster file=370, common to both=311
[1]  62 311
[1] "AMP PEAK  1(1P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           77                           234 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           77                           234 
[1] "AMP PEAK  2(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        241                          70 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        241                          70 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          231                            80 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          231                            80 
[1] "AMP PEAK  4(2P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           57                           254 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           57                           254 
[1] "AMP PEAK  5(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           57                           254 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           57                           254 
[1] "AMP PEAK  6(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            66                            245 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            66                            245 
[1] "AMP PEAK  7(4P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         43                         268 
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         43                         268 
[1] "AMP PEAK  8(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           137                            174 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           137                            174 
[1] "AMP PEAK  9(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                          112                           199 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                          112                           199 
[1] "AMP PEAK 10(6P25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                          134                           177 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                          134                           177 
[1] "AMP PEAK 11(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                          133                           178 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                          133                           178 
[1] "AMP PEAK 12(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         89                         222 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         89                         222 
[1] "AMP PEAK 13(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         67                         244 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         67                         244 
[1] "AMP PEAK 14(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                           99                           212 
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                           99                           212 
[1] "AMP PEAK 15(8Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                          177                           134 
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                          177                           134 
[1] "AMP PEAK 16(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           199                            112 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           199                            112 
[1] "AMP PEAK 17(9Q34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           38                           273 
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           38                           273 
[1] "AMP PEAK 18(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            50                            261 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            50                            261 
[1] "AMP PEAK 19(13Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            58                            253 
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            58                            253 
[1] "AMP PEAK 20(13Q33.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            60                            251 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            60                            251 
[1] "AMP PEAK 21(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            46                            265 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            46                            265 
[1] "AMP PEAK 22(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            40                            271 
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            40                            271 
[1] "AMP PEAK 23(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           127                            184 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           127                            184 
[1] "AMP PEAK 24(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             58                             253 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             58                             253 
[1] "AMP PEAK 25(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          65                          246 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          65                          246 
[1] "AMP PEAK 26(19Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             79                             232 
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             79                             232 
[1] "AMP PEAK 27(20Q13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                            104                             207 
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                            104                             207 
[1] "AMP PEAK 28(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                            111                             200 
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                            111                             200 
[1] "AMP PEAK 29(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         71                         240 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         71                         240 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           146                            165 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           146                            165 
[1] "DEL PEAK  2(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           126                            185 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           126                            185 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           42                           269 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           42                           269 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           54                           257 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           54                           257 
[1] "DEL PEAK  5(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         62                         249 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         62                         249 
[1] "DEL PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           73                           238 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           73                           238 
[1] "DEL PEAK  7(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          148                           163 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          148                           163 
[1] "DEL PEAK  8(4Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                          149                           162 
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                          149                           162 
[1] "DEL PEAK  9(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          151                           160 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          151                           160 
[1] "DEL PEAK 10(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        117                         194 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        117                         194 
[1] "DEL PEAK 11(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                          210                           101 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                          210                           101 
[1] "DEL PEAK 12(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                        205                         106 
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                        205                         106 
[1] "DEL PEAK 13(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          127                           184 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          127                           184 
[1] "DEL PEAK 14(9Q31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                          101                           210 
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                          101                           210 
[1] "DEL PEAK 15(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             86                             225 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             86                             225 
[1] "DEL PEAK 16(10Q26.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                             90                             221 
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                             90                             221 
[1] "DEL PEAK 17(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            62                            249 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            62                            249 
[1] "DEL PEAK 18(11Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            79                            232 
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            79                            232 
[1] "DEL PEAK 19(12P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            64                            247 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            64                            247 
[1] "DEL PEAK 20(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             46                             265 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             46                             265 
[1] "DEL PEAK 21(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           151                            160 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           151                            160 
[1] "DEL PEAK 22(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                           115                            196 
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                           115                            196 
[1] "DEL PEAK 23(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                            117                             194 
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                            117                             194 
[1] "DEL PEAK 24(15Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            70                            241 
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            70                            241 
[1] "DEL PEAK 25(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                           143                            168 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                           143                            168 
[1] "DEL PEAK 26(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                           191                            120 
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                           191                            120 
[1] "DEL PEAK 27(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           163                            148 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           163                            148 
[1] "DEL PEAK 28(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            79                            232 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            79                            232 
[1] "DEL PEAK 29(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            72                            239 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            72                            239 
[1] "DEL PEAK 30(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            23                            288 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            23                            288 
[1] "DEL PEAK 31(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            66                            245 
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            66                            245 
[1] "DEL PEAK 32(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             70                             241 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             70                             241 
[1] "DEL PEAK 33(XQ26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           57                           254 
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           57                           254 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 311 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
         216          328          322           20           NA          849 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
          NA           NA           NA           NA           NA         1351 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
         421            8          680          289          444          387 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-BW-A5NP TCGA-BW-A5NQ 
         227          409          146           20           NA           NA 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
           2           NA           12           NA           NA           NA 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
          NA            3            2            3            4           NA 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
          NA           NA           NA           NA           NA           NA 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
          NA           NA           NA           NA           NA           NA 
TCGA-CC-A9FU TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
          NA         2425           NA           NA           NA         3437 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
          NA           79           NA          662           NA           NA 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
        2415         2017          602         2301          204           NA 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
          NA         1495          183          887           NA           NA 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
          NA           NA         1008          989         2232          942 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
         917          816          928           NA         1711           NA 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
        2245         3308           NA           NA           NA         2398 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
         334           NA          230          334           44          843 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
        3071           NA           NA          347         2000         1800 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
          NA           NA         1931           NA           NA           NA 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
        1618         1828            9           58         1769          400 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
         436         1475         1240         1157          170           NA 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
         137          564          658         1029         1037          672 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
         959          930          890           NA          864           NA 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
         763          730          734          636           NA          527 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
          92          120          161         1742          216          252 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
         203          294          300          293          288          300 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
         259          141          382          344          386          450 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
         370          470          498          476          476         1067 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
        2405         2406         2198         1823         1882         1867 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
        1718         1788         1699         1644         1505         1451 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
         408          386          482          423          406            7 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
           6            6            6            6          400          408 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
           6            6            6          570          608          357 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
         334           NA          303          363           NA           NA 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
         987          729           NA          848           NA           NA 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
           4            1           10         1836           12           37 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1553         1636          860          935         1779           NA 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
         655          673          780          180          594          585 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 
         447          364          621          520          236           NA 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
         366          182           NA           NA          342          260 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
          NA          295          279           NA           NA           92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
          NA           NA           NA           NA          631          519 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
         122           NA          360          407          741          387 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
         180          130          291          507          559          391 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
         630          330           NA          498          135           NA 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
          62          640          579          468          472          734 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
         455          526          438           NA          486           NA 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
         253          139           31           30          122           NA 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
         142          782          706          717           21          743 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
         395           NA         1066         2258          250 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=89,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=188,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=28,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "COMPLETENESS.OF.RESECTION"
 [9] "RACE"                      "ETHNICITY"                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 311 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1 154  78  64  12 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
  155    78    64    12 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1 154  78  64  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
  155    78    64    12 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P22.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P22.3) MUTATED    43  25
  AMP PEAK  1(1P22.3) WILD-TYPE 157  67
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           68                           224 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           25                            67 
$`AMP PEAK  1(1P22.3) MUTATED`
TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 
       10.59        37.32        46.78        27.52         2.99        44.42 
TCGA-BC-A217 TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB 
       13.84         7.46         0.66         0.39         4.24         0.10 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EH 
       79.73        37.78         7.33         2.60        21.76        49.15 
TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 
       29.16        55.69         5.62         7.66        13.78        30.61 
TCGA-DD-A4NJ TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACH TCGA-DD-AACI 
       30.51       100.96         0.53        59.18         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACS TCGA-DD-AAD0 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       60.10        48.49         4.50        28.41         3.78        25.08 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       20.91         0.39        57.27         6.67         9.67         9.86 
TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 
       12.56        15.65        58.78        55.86        54.05        13.41 
TCGA-ED-A4XI TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-FV-A496 
       12.69         0.20         0.20         0.20        10.98         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       60.36         1.22        30.74        19.23        14.70        11.97 
TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-UB-A7MB TCGA-UB-A7MC 
       12.03         1.84        11.80        11.84        17.29        14.40 
TCGA-UB-A7MF TCGA-UB-AA0U 
        7.04         8.32 

$`AMP PEAK  1(1P22.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.78         0.66        48.99        27.91        10.13 
TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3EP 
        0.26        22.36         9.50        14.60        12.72        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        4.80         0.07         2.86         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B 
        0.07         0.13        83.57        53.33       113.00         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        12.95        45.11         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       21.14        19.76        25.81        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      102.74       107.11         0.36        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        26.83        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       13.48        11.41        65.75        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       12.00        15.42         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 
       14.33        40.77        38.04         5.59         5.62        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO 
       29.26        13.97        24.00        24.13        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE2 
        3.95         5.29         7.10         8.28         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
        9.86         8.52         4.64        11.31        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       12.16        15.45        16.37        15.65        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.10        72.26        59.93        61.87        61.38        56.48 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       49.48        47.70        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15        13.41         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        32.45        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T 
        8.12         6.38         0.13         0.03         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       25.64         5.92        19.53        20.42        17.10         7.76 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        5.98        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72         5.92         4.27         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85        20.71        10.85        58.88        16.37         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       21.01         2.04        21.04        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L 
       24.13        14.96         1.71        15.98         4.57         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99         4.01        13.55         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                       100.96                        113.00 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                       13.050                        15.175 
[1] "0.1 - 101.0 (13.1)" "0.0 - 113.0 (15.2)"
[1] "hr=" "1.3"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  1(1P22.3) MUTATED        29       16         1         17
  AMP PEAK  1(1P22.3) WILD-TYPE     117       56         1         35
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  1(1P22.3) MUTATED            4          3        2         0
  AMP PEAK  1(1P22.3) WILD-TYPE          3          4        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK  1(1P22.3) MUTATED           1
  AMP PEAK  1(1P22.3) WILD-TYPE         1
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  STAGE I                             29                           117
  STAGE II                            16                            56
  STAGE III                            1                             1
  STAGE IIIA                          17                            35
  STAGE IIIB                           4                             3
  STAGE IIIC                           3                             4
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] 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(1P22.3) MUTATED      30  19  23   5
  AMP PEAK  1(1P22.3) WILD-TYPE   125  59  41   7
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  T0+T1                          30                           125
  T2                             19                            59
  T3                             23                            41
  T4                              5                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED    55   1
  AMP PEAK  1(1P22.3) WILD-TYPE 167   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     55    1
  AMP PEAK  1(1P22.3) WILD-TYPE  167    2
   clus
vv  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  0                          55                           167
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  1(1P22.3) MUTATED    61   3  13
  AMP PEAK  1(1P22.3) WILD-TYPE 177   1  56
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  M0                          61                           177
  M1                           3                             1
  MX                          13                            56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED    27  50
  AMP PEAK  1(1P22.3) WILD-TYPE  73 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     27   50
  AMP PEAK  1(1P22.3) WILD-TYPE   73  161
        clus
vv       AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  FEMALE                          27                            73
  MALE                            50                           161
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                         0
  AMP PEAK  1(1P22.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                         76
  AMP PEAK  1(1P22.3) WILD-TYPE                      227
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  1(1P22.3) MUTATED                                  1
  AMP PEAK  1(1P22.3) WILD-TYPE                                5
D1V8, multiclass
                                  clus
vv                                 AMP PEAK  1(1P22.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  76
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK  1(1P22.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   227
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             5
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P22.3) MUTATED    64   6   1   6
  AMP PEAK  1(1P22.3) WILD-TYPE 210   8   0  10
D1V9, multiclass
    clus
vv   AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  R0                          64                           210
  R1                           6                             8
  R2                           1                             0
  RX                           6                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1P22.3) MUTATED                                  0    42
  AMP PEAK  1(1P22.3) WILD-TYPE                                1    99
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P22.3) MUTATED                           3    30
  AMP PEAK  1(1P22.3) WILD-TYPE                        12   115
D1V10, multiclass
                                  clus
vv                                 AMP PEAK  1(1P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     42
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     30
                                  clus
vv                                 AMP PEAK  1(1P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       99
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED     2  70
  AMP PEAK  1(1P22.3) WILD-TYPE   6 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED      2   70
  AMP PEAK  1(1P22.3) WILD-TYPE    6  217
                        clus
vv                       AMP PEAK  1(1P22.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          70
                        clus
vv                       AMP PEAK  1(1P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           217
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q22) MUTATION ANALYSIS
D2V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  2(1Q22) MUTATED   153  73
  AMP PEAK  2(1Q22) WILD-TYPE  47  19
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                        226                          66 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                         73                          19 
$`AMP PEAK  2(1Q22) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
       10.78        10.59         0.66        37.32        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A216 
       27.52         2.99        23.34         1.12         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       13.84        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.80         0.66         0.07         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF 
       51.29        90.71        79.40        66.31         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 
       55.69         5.62        19.76        25.81         7.66        17.59 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       13.78         0.36        30.61        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV 
       30.51        39.78        29.56        73.81         0.30        78.84 
TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
        9.30        10.98        27.72       100.96        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       11.41        59.18        55.40        63.48        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       53.19        60.10         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        33.83        34.09        31.53        30.58 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       13.97        28.41         3.78        25.08        24.00        24.13 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADU 
       20.91         0.39         3.02         3.95        57.27         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 
        6.67         9.67         9.86         9.63         9.86         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.45        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.26        59.93        61.38        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y 
       49.48        47.70        13.41        12.69        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20        13.15        13.41         0.20 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        11.93        14.40        32.45        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        8.12         0.13         0.03         0.33        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        14.70        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       12.03         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        9.17         0.89         2.14         3.02         1.02         2.66 
TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       37.71         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       12.72         5.92         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH 
       20.71        16.37         4.44         2.04        21.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.98         7.04         8.32         1.02         0.99         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       13.55         4.67        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       12.99        45.57        35.05         8.22 

$`AMP PEAK  2(1Q22) WILD-TYPE`
TCGA-4R-AA8I TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 
        7.10        48.99        27.91        46.78        25.32        69.57 
TCGA-BC-A3KF TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-A3M9 TCGA-DD-A116 TCGA-DD-A1EC 
        0.26        13.45         2.86         0.10        53.33        19.79 
TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       75.65         6.02        70.06        20.12       102.74       107.11 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       33.14        32.52        73.38        56.25       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-AACA TCGA-DD-AACD 
       80.75        10.98         7.56         1.45        65.75        12.53 
TCGA-DD-AACG TCGA-DD-AACK TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADN TCGA-DD-AADQ 
       15.42         0.30        22.09        29.26        17.33         5.29 
TCGA-DD-AADS TCGA-DD-AAE2 TCGA-DD-AAEE TCGA-DD-AAVU TCGA-DD-AAVX TCGA-ED-A5KG 
        7.10         9.47        16.37        61.87        56.48        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 
       13.91         0.20         0.20        22.85        27.88         6.38 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ 
        0.39        51.06        28.27        25.64         5.92        11.97 
TCGA-G3-A7M7 TCGA-GJ-A9DB TCGA-K7-A5RF TCGA-K7-A5RG TCGA-LG-A9QD TCGA-MR-A8JO 
        5.98         2.20        20.75        17.06         4.27        10.85 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-RC-A7SF TCGA-UB-AA0V TCGA-ZP-A9CY TCGA-ZS-A9CF 
       58.88        21.01        19.04         4.57        25.71        74.24 

  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                     113.00                      108.76 
  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE 
                     13.710                      19.415 
[1] "0.0 - 113.0 (13.7)" "0.1 - 108.8 (19.4)"
[1] "hr=" "1.6"
D2V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q22) MUTATED       109       60         1         38          6
  AMP PEAK  2(1Q22) WILD-TYPE      37       12         1         14          1
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(1Q22) MUTATED            5        2         1         2
  AMP PEAK  2(1Q22) WILD-TYPE          2        0         0         0
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  STAGE I                          109                          37
  STAGE II                          60                          12
  STAGE III                          1                           1
  STAGE IIIA                        38                          14
  STAGE IIIB                         6                           1
  STAGE IIIC                         5                           2
  STAGE IV                           2                           0
  STAGE IVA                          1                           0
  STAGE IVB                          2                           0
[1] 9 2
[1] 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(1Q22) MUTATED     116  65  48  10
  AMP PEAK  2(1Q22) WILD-TYPE    39  13  16   2
D2V4, multiclass
       clus
vv      AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  T0+T1                       116                          39
  T2                           65                          13
  T3                           48                          16
  T4                           10                           2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED   174   2
  AMP PEAK  2(1Q22) WILD-TYPE  48   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED    174    2
  AMP PEAK  2(1Q22) WILD-TYPE   48    1
   clus
vv  AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  0                       174                          48
  1                         2                           1
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK  2(1Q22) MUTATED   187   4  50
  AMP PEAK  2(1Q22) WILD-TYPE  51   0  19
D2V6, multiclass
    clus
vv   AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  M0                       187                          51
  M1                         4                           0
  MX                        50                          19
[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"
D2V7, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED    79 162
  AMP PEAK  2(1Q22) WILD-TYPE  21  49
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED     79  162
  AMP PEAK  2(1Q22) WILD-TYPE   21   49
        clus
vv       AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  FEMALE                        79                          21
  MALE                         162                          49
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK  2(1Q22) MUTATED                         0                      237
  AMP PEAK  2(1Q22) WILD-TYPE                       2                       66
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  2(1Q22) MUTATED                                  4
  AMP PEAK  2(1Q22) WILD-TYPE                                2
D2V8, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q22) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               237
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         4
                                  clus
vv                                 AMP PEAK  2(1Q22) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                  66
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
[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"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  2(1Q22) MUTATED   210  12   1  13
  AMP PEAK  2(1Q22) WILD-TYPE  64   2   0   3
D2V9, multiclass
    clus
vv   AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  R0                       210                          64
  R1                        12                           2
  R2                         1                           0
  RX                        13                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1Q22) MUTATED                                  1   115
  AMP PEAK  2(1Q22) WILD-TYPE                                0    26
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q22) MUTATED                          12   104
  AMP PEAK  2(1Q22) WILD-TYPE                         3    41
D2V10, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                  115
  BLACK OR AFRICAN AMERICAN                               12
  WHITE                                                  104
                                  clus
vv                                 AMP PEAK  2(1Q22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     26
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     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"
D2V11, binary
                             cls
clus                            0   1
  AMP PEAK  2(1Q22) MUTATED     6 221
  AMP PEAK  2(1Q22) WILD-TYPE   2  66
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q22) MUTATED      6  221
  AMP PEAK  2(1Q22) WILD-TYPE    2   66
                        clus
vv                       AMP PEAK  2(1Q22) MUTATED AMP PEAK  2(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             6                           2
  NOT HISPANIC OR LATINO                       221                          66
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q42.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q42.3) MUTATED   149  67
  AMP PEAK  3(1Q42.3) WILD-TYPE  51  25
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          216                            76 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           67                            25 
$`AMP PEAK  3(1Q42.3) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
       10.78        10.59         0.66        37.32        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       27.52        23.34         5.03        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5261 
        9.50        14.60        12.72         4.80         0.66         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        3.39         4.24         0.10         0.07         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       37.78       113.00         7.33         2.60         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       90.71        79.40         6.71        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 
       25.81         7.66        17.59       102.74        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.51        39.78        29.56        73.81        12.26         0.30 
TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       78.84        10.98         1.45        27.72       100.96        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        59.18        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM 
       12.00         6.41        53.19        60.10         1.91        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       13.15        14.33        48.49        40.77        38.04         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        33.83        34.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       31.53        30.58        28.41         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR 
       24.13        20.91         0.39         3.02         3.95        57.27 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 
        8.28         6.67         9.67         9.86         9.63         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.65        15.65        35.08        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       59.93        61.38        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       47.70        13.41        12.69        15.85        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20        13.15        13.41         0.20 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        11.93        14.40        32.45        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25W 
        8.12         0.13         0.03         0.33         1.22        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK 
       58.49        14.86        21.53        22.13        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 
       14.70        20.42        17.10         7.76        12.03         1.84 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
        8.55        11.80         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        3.02         2.66        37.71         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E 
       13.38        24.36        12.72         5.92         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF 
       18.38        12.85        20.71        10.85         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA 
        2.04        21.04        19.04        15.39        24.13        14.96 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L 
       14.40         1.71        15.98         7.04         8.32         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        0.99         4.01         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
        0.69        24.43        12.99        45.57        35.05         8.22 

$`AMP PEAK  3(1Q42.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X 
        7.10        48.99        27.91        46.78         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5258 
        1.12        69.57         0.26         7.46        13.45         0.07 
TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11C 
        2.86         3.32         0.10        83.57        53.33        21.76 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A2 
       66.31        19.79        75.65         6.02        55.69        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4ND TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS 
       20.12       107.11        73.38        56.25       108.76        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-AACA TCGA-DD-AACG TCGA-DD-AACK 
       10.98         9.30         7.56        65.75        15.42         0.30 
TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
       22.09        29.26        13.97        17.33         5.29         7.10 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEE TCGA-DD-AAVU TCGA-DD-AAVX 
        9.47         9.86         8.52        16.37        61.87        56.48 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 
       13.91         0.20         0.20        22.85        27.88         6.38 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH 
       60.36         0.39        51.06        53.79        28.27        25.64 
TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        5.92        11.97         5.98        11.24         1.02         2.20 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-LG-A9QD TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7SK 
       20.75        17.06         4.27        58.88        16.37        15.52 
TCGA-UB-A7MB TCGA-UB-AA0V TCGA-YA-A8S7 TCGA-ZS-A9CF 
       17.29         4.57        13.55        74.24 

  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       113.00                        108.76 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       14.085                        16.370 
[1] "0.0 - 113.0 (14.1)" "0.1 - 108.8 (16.4)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  3(1Q42.3) MUTATED       102       59         2         34
  AMP PEAK  3(1Q42.3) WILD-TYPE      44       13         0         18
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  3(1Q42.3) MUTATED            7          5        2         1
  AMP PEAK  3(1Q42.3) WILD-TYPE          0          2        0         0
                               vv
clus                            STAGE IVB
  AMP PEAK  3(1Q42.3) MUTATED           2
  AMP PEAK  3(1Q42.3) WILD-TYPE         0
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  STAGE I                            102                            44
  STAGE II                            59                            13
  STAGE III                            2                             0
  STAGE IIIA                          34                            18
  STAGE IIIB                           7                             0
  STAGE IIIC                           5                             2
  STAGE IV                             2                             0
  STAGE IVA                            1                             0
  STAGE IVB                            2                             0
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  3(1Q42.3) MUTATED     110  65  45   9
  AMP PEAK  3(1Q42.3) WILD-TYPE    45  13  19   3
D3V4, multiclass
       clus
vv      AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T0+T1                         110                            45
  T2                             65                            13
  T3                             45                            19
  T4                              9                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED   168   3
  AMP PEAK  3(1Q42.3) WILD-TYPE  54   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED    168    3
  AMP PEAK  3(1Q42.3) WILD-TYPE   54    0
   clus
vv  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  0                         168                            54
  1                           3                             0
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  3(1Q42.3) MUTATED   181   4  46
  AMP PEAK  3(1Q42.3) WILD-TYPE  57   0  23
D3V6, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  M0                         181                            57
  M1                           4                             0
  MX                          46                            23
[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"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED    76 155
  AMP PEAK  3(1Q42.3) WILD-TYPE  24  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     76  155
  AMP PEAK  3(1Q42.3) WILD-TYPE   24   56
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                          76                            24
  MALE                           155                            56
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  3(1Q42.3) MUTATED                         2
  AMP PEAK  3(1Q42.3) WILD-TYPE                       0
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  3(1Q42.3) MUTATED                        225
  AMP PEAK  3(1Q42.3) WILD-TYPE                       78
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  3(1Q42.3) MUTATED                                  4
  AMP PEAK  3(1Q42.3) WILD-TYPE                                2
D3V8, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q42.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 225
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
                                  clus
vv                                 AMP PEAK  3(1Q42.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    78
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1Q42.3) MUTATED   204  10   1  11
  AMP PEAK  3(1Q42.3) WILD-TYPE  70   4   0   5
D3V9, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  R0                         204                            70
  R1                          10                             4
  R2                           1                             0
  RX                          11                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(1Q42.3) MUTATED                                  1   110
  AMP PEAK  3(1Q42.3) WILD-TYPE                                0    31
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q42.3) MUTATED                          12   101
  AMP PEAK  3(1Q42.3) WILD-TYPE                         3    44
D3V10, multiclass
                                  clus
vv                                 AMP PEAK  3(1Q42.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    110
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    101
                                  clus
vv                                 AMP PEAK  3(1Q42.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       31
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                       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"
D3V11, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.3) MUTATED     4 214
  AMP PEAK  3(1Q42.3) WILD-TYPE   4  73
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      4  214
  AMP PEAK  3(1Q42.3) WILD-TYPE    4   73
                        clus
vv                       AMP PEAK  3(1Q42.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         214
                        clus
vv                       AMP PEAK  3(1Q42.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            73
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P24.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P24.1) MUTATED    28  22
  AMP PEAK  4(2P24.1) WILD-TYPE 172  70
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           50                           242 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                           22                            70 
$`AMP PEAK  4(2P24.1) MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A5W4 
       48.99        37.32        10.13        27.52         5.03         9.50 
TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A 
        0.66         4.24         0.10        79.73        83.57         2.60 
TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 
       90.71        45.11        29.16        13.64        55.69        30.61 
TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       33.14        73.81         9.30        10.98         1.45        27.72 
TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AAD6 TCGA-DD-AADF TCGA-DD-AADN 
       13.48        59.18        53.19        22.09         3.78        17.33 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AAE2 TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O6 
        3.02        57.27         9.47         0.20        13.41         0.20 
TCGA-EP-A2KA TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A7M9 
       11.74        22.85        51.06        30.74        21.53         1.84 
TCGA-G3-AAV0 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-LG-A6GG TCGA-UB-A7MA TCGA-UB-A7MB 
        8.55         0.89         2.14        12.72        14.96        17.29 
TCGA-WJ-A86L TCGA-ZS-A9CF 
        1.02        74.24 

$`AMP PEAK  4(2P24.1) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10S 
        7.10        10.78        10.59         0.66        27.91        46.78 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84         0.26        22.36        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        7.46        13.45         4.80         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        3.39         3.32         0.07         0.10         0.13        37.78 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       49.15         6.02        18.35        21.14         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11        13.78         0.36        32.52        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73C TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
        7.56       100.96         0.53        11.41        65.75        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ 
       12.53        63.48        12.00        15.42         6.41        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         1.91        58.16        13.15        14.33        48.49 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       40.77        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        33.83        34.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       13.97        28.41        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        0.39         3.95         5.29         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.67         9.86         9.63         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
        0.20        13.15         0.20         0.20        18.74        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        60.36         0.39         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 
        7.76        12.03         5.98        11.24        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        9.17         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06         4.01         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       24.36         5.92         4.27         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85        20.71        10.85        58.88        16.37         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       21.01         2.04        21.04        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       24.13        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         0.99         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       35.05         8.22 

  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                        90.71                        113.00 
  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE 
                         14.3                          14.5 
[1] "0.1 - 90.7 (14.3)"  "0.0 - 113.0 (14.5)"
[1] "hr=" "1.4"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  4(2P24.1) MUTATED        20       11         0         16
  AMP PEAK  4(2P24.1) WILD-TYPE     126       61         2         36
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  4(2P24.1) MUTATED            2          2        1         0
  AMP PEAK  4(2P24.1) WILD-TYPE          5          5        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK  4(2P24.1) MUTATED           1
  AMP PEAK  4(2P24.1) WILD-TYPE         1
D4V3, multiclass
            clus
vv           AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  STAGE I                             20                           126
  STAGE II                            11                            61
  STAGE III                            0                             2
  STAGE IIIA                          16                            36
  STAGE IIIB                           2                             5
  STAGE IIIC                           2                             5
  STAGE IV                             1                             1
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] 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(2P24.1) MUTATED      21  14  20   2
  AMP PEAK  4(2P24.1) WILD-TYPE   134  64  44  10
D4V4, multiclass
       clus
vv      AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  T0+T1                          21                           134
  T2                             14                            64
  T3                             20                            44
  T4                              2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.1) MUTATED    38   2
  AMP PEAK  4(2P24.1) WILD-TYPE 184   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     38    2
  AMP PEAK  4(2P24.1) WILD-TYPE  184    1
   clus
vv  AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  0                          38                           184
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  4(2P24.1) MUTATED    41   2  14
  AMP PEAK  4(2P24.1) WILD-TYPE 197   2  55
D4V6, multiclass
    clus
vv   AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  M0                          41                           197
  M1                           2                             2
  MX                          14                            55
[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"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.1) MUTATED    27  30
  AMP PEAK  4(2P24.1) WILD-TYPE  73 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED     27   30
  AMP PEAK  4(2P24.1) WILD-TYPE   73  181
        clus
vv       AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  FEMALE                          27                            73
  MALE                            30                           181
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  4(2P24.1) MUTATED                         0
  AMP PEAK  4(2P24.1) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  4(2P24.1) MUTATED                         55
  AMP PEAK  4(2P24.1) WILD-TYPE                      248
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  4(2P24.1) MUTATED                                  2
  AMP PEAK  4(2P24.1) WILD-TYPE                                4
D4V8, multiclass
                                  clus
vv                                 AMP PEAK  4(2P24.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  55
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK  4(2P24.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   248
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(2P24.1) MUTATED    48   5   0   4
  AMP PEAK  4(2P24.1) WILD-TYPE 226   9   1  12
D4V9, multiclass
    clus
vv   AMP PEAK  4(2P24.1) MUTATED AMP PEAK  4(2P24.1) WILD-TYPE
  R0                          48                           226
  R1                           5                             9
  R2                           0                             1
  RX                           4                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(2P24.1) MUTATED                                  0    21
  AMP PEAK  4(2P24.1) WILD-TYPE                                1   120
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P24.1) MUTATED                           3    33
  AMP PEAK  4(2P24.1) WILD-TYPE                        12   112
D4V10, multiclass
                                  clus
vv                                 AMP PEAK  4(2P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     21
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     33
                                  clus
vv                                 AMP PEAK  4(2P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      120
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P24.1) MUTATED     2  54
  AMP PEAK  4(2P24.1) WILD-TYPE   6 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P24.1) MUTATED      2   54
  AMP PEAK  4(2P24.1) WILD-TYPE    6  233
                        clus
vv                       AMP PEAK  4(2P24.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       AMP PEAK  4(2P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           233
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(2Q33.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(2Q33.1) MUTATED    30  21
  AMP PEAK  5(2Q33.1) WILD-TYPE 170  71
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           51                           241 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                           21                            71 
$`AMP PEAK  5(2Q33.1) MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A8YO 
       48.99        37.32        10.13        23.34        13.84         7.46 
TCGA-DD-A113 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       79.73        21.76        90.71        29.16        13.64        55.69 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A 
      102.74        13.78        30.61        10.98         1.45        13.48 
TCGA-DD-AACB TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 
       59.18         6.41        53.19         5.62        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADU 
       31.53        13.97         3.78        24.00         3.02         8.28 
TCGA-DD-AADW TCGA-DD-AAE6 TCGA-DD-AAEE TCGA-DD-AAVS TCGA-ED-A7PY TCGA-ED-A82E 
        6.67         4.64        16.37        59.93         0.20        13.41 
TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-ES-A2HS TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T 
        0.20        11.74        22.85         0.03         1.22        51.06 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A5SM TCGA-G3-AAV6 TCGA-LG-A6GG TCGA-RC-A7SK 
       30.74        21.53        17.10         2.14        12.72        15.52 
TCGA-UB-A7MA TCGA-YA-A8S7 TCGA-ZS-A9CF 
       14.96        13.55        74.24 

$`AMP PEAK  5(2Q33.1) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10S 
        7.10        10.78        10.59         0.66        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 
       27.52        27.52         2.99        25.32         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        44.42         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72        13.45         4.80         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.39         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         2.60         0.46        51.29        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        18.35        21.14         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 
        7.66        70.06        17.59        20.12       107.11         0.36 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        73.38        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        7.56        27.72       100.96         0.53        11.41        65.75 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACJ 
       55.40        12.53        63.48        12.00        15.42        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         1.91        58.16        13.15        14.33        48.49 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       40.77        38.04         5.59         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADK 
       33.83        30.58        29.26        28.41        25.08        24.13 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        17.33         3.95         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
        7.10         9.67         9.86         9.63         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        8.52        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.45        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.26        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB 
       13.15         0.20         0.20        18.74        19.99        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        11.93        14.40        32.45        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
       19.10        27.88         8.12         6.38         0.13         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
       60.36         0.39        53.79        28.27        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       11.97        20.42         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MB 
        2.04        21.04        19.04        15.39        24.13        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       14.40         1.71        15.98         7.04         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        1.02         0.99         4.01         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CG 
        8.22 

  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                       102.74                        113.00 
  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE 
                        14.96                         14.40 
[1] "0.0 - 102.7 (15.0)" "0.1 - 113.0 (14.4)"
[1] "hr=" "1.3"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  5(2Q33.1) MUTATED        21       15         1         11
  AMP PEAK  5(2Q33.1) WILD-TYPE     125       57         1         41
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  5(2Q33.1) MUTATED            2          2        1         0
  AMP PEAK  5(2Q33.1) WILD-TYPE          5          5        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK  5(2Q33.1) MUTATED           1
  AMP PEAK  5(2Q33.1) WILD-TYPE         1
D5V3, multiclass
            clus
vv           AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  STAGE I                             21                           125
  STAGE II                            15                            57
  STAGE III                            1                             1
  STAGE IIIA                          11                            41
  STAGE IIIB                           2                             5
  STAGE IIIC                           2                             5
  STAGE IV                             1                             1
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] 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(2Q33.1) MUTATED      22  17  15   3
  AMP PEAK  5(2Q33.1) WILD-TYPE   133  61  49   9
D5V4, multiclass
       clus
vv      AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  T0+T1                          22                           133
  T2                             17                            61
  T3                             15                            49
  T4                              3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED    43   1
  AMP PEAK  5(2Q33.1) WILD-TYPE 179   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     43    1
  AMP PEAK  5(2Q33.1) WILD-TYPE  179    2
   clus
vv  AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  0                          43                           179
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  5(2Q33.1) MUTATED    46   2   9
  AMP PEAK  5(2Q33.1) WILD-TYPE 192   2  60
D5V6, multiclass
    clus
vv   AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  M0                          46                           192
  M1                           2                             2
  MX                           9                            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED    31  26
  AMP PEAK  5(2Q33.1) WILD-TYPE  69 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED     31   26
  AMP PEAK  5(2Q33.1) WILD-TYPE   69  185
        clus
vv       AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  FEMALE                          31                            69
  MALE                            26                           185
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  5(2Q33.1) MUTATED                         0
  AMP PEAK  5(2Q33.1) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  5(2Q33.1) MUTATED                         55
  AMP PEAK  5(2Q33.1) WILD-TYPE                      248
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  5(2Q33.1) MUTATED                                  2
  AMP PEAK  5(2Q33.1) WILD-TYPE                                4
D5V8, multiclass
                                  clus
vv                                 AMP PEAK  5(2Q33.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  55
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK  5(2Q33.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   248
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(2Q33.1) MUTATED    51   4   0   2
  AMP PEAK  5(2Q33.1) WILD-TYPE 223  10   1  14
D5V9, multiclass
    clus
vv   AMP PEAK  5(2Q33.1) MUTATED AMP PEAK  5(2Q33.1) WILD-TYPE
  R0                          51                           223
  R1                           4                            10
  R2                           0                             1
  RX                           2                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(2Q33.1) MUTATED                                  0    26
  AMP PEAK  5(2Q33.1) WILD-TYPE                                1   115
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(2Q33.1) MUTATED                           1    29
  AMP PEAK  5(2Q33.1) WILD-TYPE                        14   116
D5V10, multiclass
                                  clus
vv                                 AMP PEAK  5(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     26
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     29
                                  clus
vv                                 AMP PEAK  5(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      115
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q33.1) MUTATED     2  53
  AMP PEAK  5(2Q33.1) WILD-TYPE   6 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q33.1) MUTATED      2   53
  AMP PEAK  5(2Q33.1) WILD-TYPE    6  234
                        clus
vv                       AMP PEAK  5(2Q33.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       AMP PEAK  5(2Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           234
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(3Q26.31) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(3Q26.31) MUTATED    38  23
  AMP PEAK  6(3Q26.31) WILD-TYPE 162  69
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            61                            231 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                            23                             69 
$`AMP PEAK  6(3Q26.31) MUTATED`
TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A217 
        0.66        10.13        27.52        23.34         1.12        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-A3MA 
       22.36         9.50        14.60        13.45         0.66         0.07 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL 
       37.78        83.57        21.76        12.95        29.16        13.64 
TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NI TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-A73G 
        5.62       102.74        26.83        78.84         1.45       100.96 
TCGA-DD-AA3A TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACZ 
       13.48        15.42         1.91        48.49        38.04         5.62 
TCGA-DD-AAD5 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR 
       34.09        13.97        28.41        20.91        17.33        57.27 
TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEK TCGA-DD-AAVS 
        8.28         9.63         4.64        12.69        35.08        59.93 
TCGA-DD-AAW0 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KA TCGA-ES-A2HS 
       54.05         0.20         0.20        13.41        11.74        22.85 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25X TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-KR-A7K8 
        6.38         0.03        58.49         1.84         1.02        24.36 
TCGA-LG-A9QD TCGA-MI-A75G TCGA-PD-A5DF TCGA-UB-A7MC TCGA-UB-A7MD TCGA-WJ-A86L 
        4.27        18.38        21.01        14.40         1.71         1.02 
TCGA-ZS-A9CF 
       74.24 

$`AMP PEAK  6(3Q26.31) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59        48.99        27.91        37.32 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 
       46.78        27.52         2.99        25.32        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 
       44.42         0.26        12.72         7.46         4.80         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.13        79.73        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65         6.71        45.11        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        21.14        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        17.59        20.12       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       10.98        27.72         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        63.48        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU 
       60.10         0.30        58.16        13.15        14.33        40.77 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
        5.59         4.50        18.54        21.63        33.83        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       31.53        30.58        29.26         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
       24.13         0.39         3.02         3.95         5.29         7.10 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
        6.67         9.67         9.86         9.47         9.86         8.52 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       12.56        11.31        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU 
       15.65        15.65        79.07        79.10        72.26        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW2 TCGA-DD-AAW3 
       61.38        56.48        58.78        55.86        49.48        47.70 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        10.98         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        32.45        23.97        19.10        27.88         8.12 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.13         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       20.42        17.10         7.76        12.03         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
        8.55        11.80         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        3.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC 
        4.01         2.14        11.84        13.38        12.72         5.92 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
       16.37         4.44         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-A7MF 
       15.52        24.13        14.96        17.29        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
        8.32         4.57         0.99         4.01        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       45.57        35.05         8.22 

  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                        102.74                         113.00 
  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE 
                         13.97                          14.79 
[1] "0.0 - 102.7 (14.0)" "0.1 - 113.0 (14.8)"
[1] "hr=" "1.3"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  6(3Q26.31) MUTATED        29       19         1         11
  AMP PEAK  6(3Q26.31) WILD-TYPE     117       53         1         41
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  6(3Q26.31) MUTATED            2          1        0         0
  AMP PEAK  6(3Q26.31) WILD-TYPE          5          6        2         1
                                vv
clus                             STAGE IVB
  AMP PEAK  6(3Q26.31) MUTATED           0
  AMP PEAK  6(3Q26.31) WILD-TYPE         2
D6V3, multiclass
            clus
vv           AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  STAGE I                              29                            117
  STAGE II                             19                             53
  STAGE III                             1                              1
  STAGE IIIA                           11                             41
  STAGE IIIB                            2                              5
  STAGE IIIC                            1                              6
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK  6(3Q26.31) MUTATED      30  19  14   3
  AMP PEAK  6(3Q26.31) WILD-TYPE   125  59  50   9
D6V4, multiclass
       clus
vv      AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  T0+T1                           30                            125
  T2                              19                             59
  T3                              14                             50
  T4                               3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    43   1
  AMP PEAK  6(3Q26.31) WILD-TYPE 179   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     43    1
  AMP PEAK  6(3Q26.31) WILD-TYPE  179    2
   clus
vv  AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  0                           43                            179
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK  6(3Q26.31) MUTATED    49   0  17
  AMP PEAK  6(3Q26.31) WILD-TYPE 189   4  52
D6V6, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  M0                           49                            189
  M1                            0                              4
  MX                           17                             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED    20  46
  AMP PEAK  6(3Q26.31) WILD-TYPE  80 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED     20   46
  AMP PEAK  6(3Q26.31) WILD-TYPE   80  165
        clus
vv       AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  FEMALE                           20                             80
  MALE                             46                            165
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK  6(3Q26.31) MUTATED                         0
  AMP PEAK  6(3Q26.31) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK  6(3Q26.31) MUTATED                         64
  AMP PEAK  6(3Q26.31) WILD-TYPE                      239
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  6(3Q26.31) MUTATED                                  2
  AMP PEAK  6(3Q26.31) WILD-TYPE                                4
D6V8, multiclass
                                  clus
vv                                 AMP PEAK  6(3Q26.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   64
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 AMP PEAK  6(3Q26.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    239
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              4
[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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(3Q26.31) MUTATED    59   2   0   4
  AMP PEAK  6(3Q26.31) WILD-TYPE 215  12   1  12
D6V9, multiclass
    clus
vv   AMP PEAK  6(3Q26.31) MUTATED AMP PEAK  6(3Q26.31) WILD-TYPE
  R0                           59                            215
  R1                            2                             12
  R2                            0                              1
  RX                            4                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(3Q26.31) MUTATED                                  0    29
  AMP PEAK  6(3Q26.31) WILD-TYPE                                1   112
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.31) MUTATED                           5    31
  AMP PEAK  6(3Q26.31) WILD-TYPE                        10   114
D6V10, multiclass
                                  clus
vv                                 AMP PEAK  6(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      29
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      31
                                  clus
vv                                 AMP PEAK  6(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       112
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.31) MUTATED     1  62
  AMP PEAK  6(3Q26.31) WILD-TYPE   7 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.31) MUTATED      1   62
  AMP PEAK  6(3Q26.31) WILD-TYPE    7  225
                        clus
vv                       AMP PEAK  6(3Q26.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           62
                        clus
vv                       AMP PEAK  6(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            225
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4P14) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(4P14) MUTATED    31   8
  AMP PEAK  7(4P14) WILD-TYPE 169  84
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                         39                         253 
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                          8                          84 
$`AMP PEAK  7(4P14) MUTATED`
TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BD-A3EP TCGA-CC-5261 TCGA-CC-A3M9 
       10.13        13.84         9.50        13.45         0.39         0.10 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A1EC TCGA-DD-A1EH 
        0.10        79.73       113.00         2.60        19.79        49.15 
TCGA-DD-A1EI TCGA-DD-A4NN TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACM 
        6.02        29.56       100.96        15.42        53.19        58.16 
TCGA-DD-AAD3 TCGA-DD-AADB TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AAED 
       33.83        29.26         3.02         3.95        57.27        15.45 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 
       72.26        59.93        13.35         0.20        13.41         0.20 
TCGA-EP-A2KA TCGA-FV-A2QR TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-LG-A6GG TCGA-QA-A7B7 
       11.74        19.10        22.13         1.84        12.72         2.04 
TCGA-RC-A7SK TCGA-WQ-A9G7 TCGA-ZS-A9CF 
       15.52         0.99        74.24 

$`AMP PEAK  7(4P14) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO 
       22.36        14.60        12.72         7.46         4.80         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        0.07         2.86         3.39         4.24         3.32         0.07 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B 
        0.13        37.78        83.57        53.33         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
       21.76        51.29        90.71        79.40        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        12.95        45.11        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO 
       30.15        26.83        30.51        39.78        56.25        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
        9.30         7.56        10.98         1.45        27.72        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        65.75        59.18        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       63.48        12.00         6.41        60.10         0.30         1.91 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       13.15        14.33        48.49        40.77        38.04         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62         4.50        18.54        21.63        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       31.53        30.58        13.97        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ 
       24.00        24.13        20.91         0.39        17.33         5.29 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
        7.10         8.28         6.67         9.67         9.86         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.47         9.86         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       12.69        14.79        12.16        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       35.08        79.07        79.10        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91         0.23         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
        0.20        13.15         0.20         0.20        18.74        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        23.97        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       20.42        17.10         7.76        12.03         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
        8.55        11.80         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        19.04        15.39        24.13        14.96        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       14.40         1.71        15.98         7.04         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        1.02         4.01        13.55         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CG 
        8.22 

  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                       0.10                        0.03 
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                     113.00                      108.76 
  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE 
                      13.84                       14.60 
[1] "0.1 - 113.0 (13.8)" "0.0 - 108.8 (14.6)"
[1] "hr=" "1.9"
D7V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(4P14) MUTATED        17       13         1          9          1
  AMP PEAK  7(4P14) WILD-TYPE     129       59         1         43          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(4P14) MUTATED            0        0         0         0
  AMP PEAK  7(4P14) WILD-TYPE          7        2         1         2
D7V3, multiclass
            clus
vv           AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  STAGE I                           17                         129
  STAGE II                          13                          59
  STAGE III                          1                           1
  STAGE IIIA                         9                          43
  STAGE IIIB                         1                           6
  STAGE IIIC                         0                           7
  STAGE IV                           0                           2
  STAGE IVA                          0                           1
  STAGE IVB                          0                           2
[1] 9 2
[1] 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(4P14) MUTATED      17  13  13   0
  AMP PEAK  7(4P14) WILD-TYPE   138  65  51  12
D7V4, multiclass
       clus
vv      AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  T0+T1                        17                         138
  T2                           13                          65
  T3                           13                          51
  T4                            0                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                             cls
clus                            0   1
  AMP PEAK  7(4P14) MUTATED    33   0
  AMP PEAK  7(4P14) WILD-TYPE 189   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED     33    0
  AMP PEAK  7(4P14) WILD-TYPE  189    3
   clus
vv  AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  0                        33                         189
  1                         0                           3
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK  7(4P14) MUTATED    38   0   5
  AMP PEAK  7(4P14) WILD-TYPE 200   4  64
D7V6, multiclass
    clus
vv   AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  M0                        38                         200
  M1                         0                           4
  MX                         5                          64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(4P14) MUTATED    15  28
  AMP PEAK  7(4P14) WILD-TYPE  85 183
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED     15   28
  AMP PEAK  7(4P14) WILD-TYPE   85  183
        clus
vv       AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  FEMALE                        15                          85
  MALE                          28                         183
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK  7(4P14) MUTATED                         0                       43
  AMP PEAK  7(4P14) WILD-TYPE                       2                      260
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  7(4P14) MUTATED                                  0
  AMP PEAK  7(4P14) WILD-TYPE                                6
D7V8, multiclass
                                  clus
vv                                 AMP PEAK  7(4P14) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                43
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         0
                                  clus
vv                                 AMP PEAK  7(4P14) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 260
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           6
[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"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  7(4P14) MUTATED    38   2   0   3
  AMP PEAK  7(4P14) WILD-TYPE 236  12   1  13
D7V9, multiclass
    clus
vv   AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  R0                        38                         236
  R1                         2                          12
  R2                         0                           1
  RX                         3                          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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(4P14) MUTATED                                  0    24
  AMP PEAK  7(4P14) WILD-TYPE                                1   117
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4P14) MUTATED                           3    16
  AMP PEAK  7(4P14) WILD-TYPE                        12   129
D7V10, multiclass
                                  clus
vv                                 AMP PEAK  7(4P14) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   24
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   16
                                  clus
vv                                 AMP PEAK  7(4P14) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    117
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                             cls
clus                            0   1
  AMP PEAK  7(4P14) MUTATED     0  42
  AMP PEAK  7(4P14) WILD-TYPE   8 245
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(4P14) MUTATED      0   42
  AMP PEAK  7(4P14) WILD-TYPE    8  245
                        clus
vv                       AMP PEAK  7(4P14) MUTATED AMP PEAK  7(4P14) WILD-TYPE
  HISPANIC OR LATINO                             0                           8
  NOT HISPANIC OR LATINO                        42                         245
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(5P15.33) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(5P15.33) MUTATED    80  47
  AMP PEAK  8(5P15.33) WILD-TYPE 120  45
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           127                            165 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            47                             45 
$`AMP PEAK  8(5P15.33) MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A10Z TCGA-BC-A112 
       10.78        37.32        10.13         2.99         1.12         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO 
       44.42        13.84        22.36         7.46        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        0.07         4.24         3.32         0.10         0.10         0.13 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 
       83.57        53.33       113.00         2.60        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V 
       79.40         6.71        12.95         6.02        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 
       55.69         5.62         7.66        17.59       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NV 
        0.36        73.38        30.51        39.78        73.81        78.84 
TCGA-DD-A73C TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACF 
        7.56       100.96        13.48         0.53        65.75        12.00 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AAD2 
       15.42        53.19        60.10        13.15         5.62        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADQ 
       34.09        31.53        13.97         3.78        17.33         5.29 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAEA 
       57.27         8.28         9.47         9.86         4.64        14.79 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAW2 
       16.37        15.65        35.08        61.87        58.78        49.48 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.41        13.35         0.23         0.20        13.15        13.41 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A23B 
        0.20        10.98         0.62         9.96        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       23.97        19.10        27.88         0.03        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ 
        1.22        51.06        30.74        58.49        22.13        19.53 
TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 
       14.70        17.10        12.03         1.84        11.24        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 
        9.70         2.14         3.02         2.20         2.66        11.84 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.72         5.92        18.38        20.71        58.88         4.44 
TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       21.01        19.04        24.13        15.98         7.04         8.32 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
        0.99         4.01        23.21         0.69        24.43        12.99 
TCGA-ZS-A9CE 
       35.05 

$`AMP PEAK  8(5P15.33) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
        7.10        10.59         0.66        48.99        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A3KF 
       27.52        27.52        25.32        23.34        69.57         0.26 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5261 
        9.50        14.60        12.72         4.80         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B 
        3.39         0.07        79.73        37.78         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH 
       21.76        66.31        19.79        75.65        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 
       29.16        18.35        19.76        25.81        70.06        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11        30.61        33.14        32.52        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       26.83        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       80.75        10.98         9.30        10.98         1.45        27.72 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACH 
       11.41        59.18        55.40        12.53        63.48         6.41 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        0.30         1.91        58.16        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 
       38.04         5.59         4.50        18.54        33.83        22.09 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       30.58        29.26        28.41        25.08        24.00        24.13 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADS TCGA-DD-AADW 
       20.91         0.39         3.02         3.95         7.10         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.67         9.86         9.63         8.52        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ 
       12.69        12.16        15.45        15.65        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.26        59.93        61.38        56.48        55.86        54.05 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       47.70        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
       11.93        22.85         8.12         6.38         0.13         0.33 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAV0 
       19.23        11.97        20.42         7.76         5.98         8.55 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        9.17         0.89         1.02        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C 
        4.01         2.14        13.38        24.36         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A7S9 
       16.67        12.85        10.85        16.37         2.04        21.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        14.96        17.29        14.40         1.71 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
        4.57         1.02        13.55         4.67        25.71        23.57 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        74.24         8.22 

  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                        113.00                         108.76 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                         13.45                          15.65 
[1] "0.0 - 113.0 (13.4)" "0.1 - 108.8 (15.7)"
[1] "hr=" "1.4"
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  8(5P15.33) MUTATED        53       35         1         30
  AMP PEAK  8(5P15.33) WILD-TYPE      93       37         1         22
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  8(5P15.33) MUTATED            4          2        1         1
  AMP PEAK  8(5P15.33) WILD-TYPE          3          5        1         0
                                vv
clus                             STAGE IVB
  AMP PEAK  8(5P15.33) MUTATED           0
  AMP PEAK  8(5P15.33) WILD-TYPE         2
D8V3, multiclass
            clus
vv           AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  STAGE I                              53                             93
  STAGE II                             35                             37
  STAGE III                             1                              1
  STAGE IIIA                           30                             22
  STAGE IIIB                            4                              3
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             1                              0
  STAGE IVB                             0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK  8(5P15.33) MUTATED      57 39 37  4
  AMP PEAK  8(5P15.33) WILD-TYPE    98 39 27  8
D8V4, multiclass
       clus
vv      AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  T0+T1                           57                             98
  T2                              39                             39
  T3                              37                             27
  T4                               4                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED    96   1
  AMP PEAK  8(5P15.33) WILD-TYPE 126   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     96    1
  AMP PEAK  8(5P15.33) WILD-TYPE  126    2
   clus
vv  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  0                           96                            126
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK  8(5P15.33) MUTATED   107   1  29
  AMP PEAK  8(5P15.33) WILD-TYPE 131   3  40
D8V6, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  M0                          107                            131
  M1                            1                              3
  MX                           29                             40
[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"
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED    44  93
  AMP PEAK  8(5P15.33) WILD-TYPE  56 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     44   93
  AMP PEAK  8(5P15.33) WILD-TYPE   56  118
        clus
vv       AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  FEMALE                           44                             56
  MALE                             93                            118
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK  8(5P15.33) MUTATED                         0
  AMP PEAK  8(5P15.33) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK  8(5P15.33) MUTATED                        134
  AMP PEAK  8(5P15.33) WILD-TYPE                      169
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  8(5P15.33) MUTATED                                  3
  AMP PEAK  8(5P15.33) WILD-TYPE                                3
D8V8, multiclass
                                  clus
vv                                 AMP PEAK  8(5P15.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  134
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK  8(5P15.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    169
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              3
[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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  8(5P15.33) MUTATED   120   7   0   7
  AMP PEAK  8(5P15.33) WILD-TYPE 154   7   1   9
D8V9, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  R0                          120                            154
  R1                            7                              7
  R2                            0                              1
  RX                            7                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(5P15.33) MUTATED                                  1    61
  AMP PEAK  8(5P15.33) WILD-TYPE                                0    80
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(5P15.33) MUTATED                           8    62
  AMP PEAK  8(5P15.33) WILD-TYPE                         7    83
D8V10, multiclass
                                  clus
vv                                 AMP PEAK  8(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      61
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      62
                                  clus
vv                                 AMP PEAK  8(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        80
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                        83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                                cls
clus                               0   1
  AMP PEAK  8(5P15.33) MUTATED     4 126
  AMP PEAK  8(5P15.33) WILD-TYPE   4 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED      4  126
  AMP PEAK  8(5P15.33) WILD-TYPE    4  161
                        clus
vv                       AMP PEAK  8(5P15.33) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          126
                        clus
vv                       AMP PEAK  8(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            161
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(5Q35.3) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(5Q35.3) MUTATED    64  41
  AMP PEAK  9(5Q35.3) WILD-TYPE 136  51
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                          105                           187 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                           41                            51 
$`AMP PEAK  9(5Q35.3) MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A216 
       10.78        37.32        27.52         2.99         5.03        44.42 
TCGA-BC-A217 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 
       13.84         3.32         0.10         0.13        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE 
      113.00         7.33        51.29        90.71        79.40         6.71 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 
       21.14        55.69         5.62         7.66        17.59       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NR 
       13.78         0.36        73.38        39.78        73.81         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACC 
       78.84        10.98       100.96        13.48         0.53        55.40 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        12.00        15.42         6.41        53.19        60.10 
TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AADC TCGA-DD-AADF 
       13.15         5.62        18.54        21.63        13.97         3.78 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR 
       25.08        24.13         0.39        17.33         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEE 
        7.10         8.28         9.86         9.63         9.86        16.37 
TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVX 
       15.65        35.08        79.07        72.26        61.87        56.48 
TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP 
       58.78        54.05        49.48         0.23         0.20        13.15 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A3I0 TCGA-FV-A3R2 
       10.98         0.62         9.96        14.40        27.88         6.38 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A3CG 
        0.03         0.39         1.22        51.06        30.74        22.13 
TCGA-G3-A5SM TCGA-G3-AAV1 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-LG-A6GG 
       17.10        11.80         2.20         2.66        11.84        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF 
        5.92         4.27         9.57        18.38        20.71        16.37 
TCGA-O8-A75V TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        4.44        19.04        24.13        14.96         0.99         4.01 
TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       23.21         0.69        35.05 

$`AMP PEAK  9(5Q35.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       46.78        27.52        25.32        23.34         1.12        69.57 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
        0.26        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45         4.80         0.66         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 
        3.39         4.24         0.10         0.07        79.73        37.78 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        2.60         0.46        21.76        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 
       13.64        19.76        25.81        70.06        20.12       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS 
       30.51        56.25        29.56       108.76        12.26        80.75 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC9 
        9.30         7.56        10.98         1.45        27.72        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       65.75        59.18        63.48         0.30         1.91        58.16 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 
       14.33        48.49        40.77        38.04         5.59         4.50 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       33.83        34.09        22.09        31.53        30.58        29.26 
TCGA-DD-AADD TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADW 
       28.41        24.00        20.91         3.02         3.95         6.67 
TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.67         9.47         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVQ 
       12.69        14.79        12.16        15.45        15.65        79.10 
TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       59.93        61.38        55.86        47.70        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.74        11.93        22.85        32.45        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A25V 
        8.12         0.13         0.33        60.36        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 
       19.23        14.70        11.97        20.42         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
        5.98         1.84        11.24         8.55         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RF 
        0.89         2.14         3.02         1.02        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-MI-A75E 
       17.06         4.01         2.14        13.38        24.36        16.67 
TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       12.85        10.85        58.88        21.01         2.04        21.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.39        15.52        17.29        14.40         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV 
        7.04         8.32         4.57         1.02        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       25.71        23.57        24.43        12.99        45.57        74.24 
TCGA-ZS-A9CG 
        8.22 

  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                       113.00                        108.76 
  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE 
                        13.97                         14.70 
[1] "0.0 - 113.0 (14.0)" "0.1 - 108.8 (14.7)"
[1] "hr=" "1.3"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK  9(5Q35.3) MUTATED        51       28         1         19
  AMP PEAK  9(5Q35.3) WILD-TYPE      95       44         1         33
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  9(5Q35.3) MUTATED            2          1        2         0
  AMP PEAK  9(5Q35.3) WILD-TYPE          5          6        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK  9(5Q35.3) MUTATED           0
  AMP PEAK  9(5Q35.3) WILD-TYPE         2
D9V3, multiclass
            clus
vv           AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  STAGE I                             51                            95
  STAGE II                            28                            44
  STAGE III                            1                             1
  STAGE IIIA                          19                            33
  STAGE IIIB                           2                             5
  STAGE IIIC                           1                             6
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] 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(5Q35.3) MUTATED      53  31  25   3
  AMP PEAK  9(5Q35.3) WILD-TYPE   102  47  39   9
D9V4, multiclass
       clus
vv      AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  T0+T1                          53                           102
  T2                             31                            47
  T3                             25                            39
  T4                              3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED    80   0
  AMP PEAK  9(5Q35.3) WILD-TYPE 142   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     80    0
  AMP PEAK  9(5Q35.3) WILD-TYPE  142    3
   clus
vv  AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  0                          80                           142
  1                           0                             3
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  9(5Q35.3) MUTATED    90   2  20
  AMP PEAK  9(5Q35.3) WILD-TYPE 148   2  49
D9V6, multiclass
    clus
vv   AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  M0                          90                           148
  M1                           2                             2
  MX                          20                            49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED    33  79
  AMP PEAK  9(5Q35.3) WILD-TYPE  67 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED     33   79
  AMP PEAK  9(5Q35.3) WILD-TYPE   67  132
        clus
vv       AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  FEMALE                          33                            67
  MALE                            79                           132
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK  9(5Q35.3) MUTATED                         0
  AMP PEAK  9(5Q35.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK  9(5Q35.3) MUTATED                        108
  AMP PEAK  9(5Q35.3) WILD-TYPE                      195
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK  9(5Q35.3) MUTATED                                  4
  AMP PEAK  9(5Q35.3) WILD-TYPE                                2
D9V8, multiclass
                                  clus
vv                                 AMP PEAK  9(5Q35.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 108
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
                                  clus
vv                                 AMP PEAK  9(5Q35.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   195
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(5Q35.3) MUTATED    99   8   1   2
  AMP PEAK  9(5Q35.3) WILD-TYPE 175   6   0  14
D9V9, multiclass
    clus
vv   AMP PEAK  9(5Q35.3) MUTATED AMP PEAK  9(5Q35.3) WILD-TYPE
  R0                          99                           175
  R1                           8                             6
  R2                           1                             0
  RX                           2                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(5Q35.3) MUTATED                                  0    55
  AMP PEAK  9(5Q35.3) WILD-TYPE                                1    86
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(5Q35.3) MUTATED                           4    49
  AMP PEAK  9(5Q35.3) WILD-TYPE                        11    96
D9V10, multiclass
                                  clus
vv                                 AMP PEAK  9(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     55
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     49
                                  clus
vv                                 AMP PEAK  9(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       86
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                       96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
                               cls
clus                              0   1
  AMP PEAK  9(5Q35.3) MUTATED     3 102
  AMP PEAK  9(5Q35.3) WILD-TYPE   5 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(5Q35.3) MUTATED      3  102
  AMP PEAK  9(5Q35.3) WILD-TYPE    5  185
                        clus
vv                       AMP PEAK  9(5Q35.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         102
                        clus
vv                       AMP PEAK  9(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           185
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6P25.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(6P25.2) MUTATED    80  43
  AMP PEAK 10(6P25.2) WILD-TYPE 120  49
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                          123                           169 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                           43                            49 
$`AMP PEAK 10(6P25.2) MUTATED`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       27.91        10.13        27.52         5.03        44.42        13.84 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 
       22.36        14.60        12.72        13.45         0.66         0.39 
TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
        4.24         0.10         0.13        37.78       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
        2.60        21.76         6.71        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A3A7 
       29.16        55.69         5.62        19.76       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN 
        0.36        30.61        30.15        30.51        39.78        29.56 
TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB 
       80.75        10.98         1.45         0.53        65.75        59.18 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        63.48        12.00         6.41        53.19        60.10 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADL 
       13.15        14.33        33.83        30.58         3.78        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADW 
        0.39        17.33         3.02         3.95         5.29         6.67 
TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAEH 
        9.86         9.47         9.86        12.69        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAW2 
       35.08        72.26        59.93        61.38        58.78        49.48 
TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 
       47.70        13.35         0.20         0.20        13.41         0.20 
TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 
        0.20        11.74        10.98         0.62        22.85        27.88 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
        6.38         0.13         0.39         1.22        53.79        58.49 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A6UC 
       14.86        22.13        19.23        14.70        20.42         7.76 
TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 
       11.80         9.17         0.89         2.14        11.84        24.36 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
       12.72        18.38        12.85        20.71        16.37         4.44 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.01        21.04        15.52        24.13        14.96        17.29 
TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       14.40        15.98         7.04         8.32         1.02         0.99 
TCGA-YA-A8S7 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       13.55        45.57        74.24 

$`AMP PEAK 10(6P25.2) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-A10Q 
        7.10        10.78        10.59         0.66        48.99        37.32 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 
       69.57         0.26         9.50         7.46         4.80         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 
        2.86         3.39         3.32         0.10         0.07        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       83.57        53.33         0.46        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       66.31        19.79        75.65         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       21.14        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI 
      107.11        33.14        32.52        73.38        30.97        26.83 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV 
       56.25        73.81       108.76        12.26         0.30        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       10.98         9.30         7.56        27.72       100.96        13.48 
TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       11.41        55.40        15.42         0.30         1.91        58.16 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       18.54        21.63        34.09        22.09        31.53        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADR 
       13.97        28.41        25.08        24.00        24.13        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE6 
        7.10         8.28         9.67         9.63         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       12.56        11.31        14.79        12.16        15.45        16.37 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 
       79.07        79.10        61.87        56.48        55.86        54.05 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91         0.23         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL 
        0.20        13.15         0.20        18.74        19.99         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        14.40        32.45        23.97        19.10         8.12 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.33        60.36        51.06        28.27        30.74 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM 
       21.53        25.64         5.92        19.53        11.97        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       12.03         5.98         1.84        11.24         8.55         9.70 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06         4.01         2.14        13.38         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-QA-A7B7 TCGA-RC-A7SF 
        9.57        16.67        10.85        58.88         2.04        19.04 
TCGA-RC-A7SH TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY 
       15.39         1.71         4.57         4.01         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       23.21        23.57         0.69        24.43        12.99        35.05 
TCGA-ZS-A9CG 
        8.22 

  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                       113.00                        108.76 
  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE 
                        14.33                         15.39 
[1] "0.1 - 113.0 (14.3)" "0.0 - 108.8 (15.4)"
[1] "hr=" "1.3"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 10(6P25.2) MUTATED        57       33         2         26
  AMP PEAK 10(6P25.2) WILD-TYPE      89       39         0         26
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(6P25.2) MUTATED            5          2        2         0
  AMP PEAK 10(6P25.2) WILD-TYPE          2          5        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK 10(6P25.2) MUTATED           1
  AMP PEAK 10(6P25.2) WILD-TYPE         1
D10V3, multiclass
            clus
vv           AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  STAGE I                             57                            89
  STAGE II                            33                            39
  STAGE III                            2                             0
  STAGE IIIA                          26                            26
  STAGE IIIB                           5                             2
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] 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(6P25.2) MUTATED      58 36 35  4
  AMP PEAK 10(6P25.2) WILD-TYPE    97 42 29  8
D10V4, multiclass
       clus
vv      AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  T0+T1                          58                            97
  T2                             36                            42
  T3                             35                            29
  T4                              4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED    95   1
  AMP PEAK 10(6P25.2) WILD-TYPE 127   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED     95    1
  AMP PEAK 10(6P25.2) WILD-TYPE  127    2
   clus
vv  AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  0                          95                           127
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 10(6P25.2) MUTATED   104   3  27
  AMP PEAK 10(6P25.2) WILD-TYPE 134   1  42
D10V6, multiclass
    clus
vv   AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  M0                         104                           134
  M1                           3                             1
  MX                          27                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED    45  89
  AMP PEAK 10(6P25.2) WILD-TYPE  55 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED     45   89
  AMP PEAK 10(6P25.2) WILD-TYPE   55  122
        clus
vv       AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  FEMALE                          45                            55
  MALE                            89                           122
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 10(6P25.2) MUTATED                         0
  AMP PEAK 10(6P25.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 10(6P25.2) MUTATED                        131
  AMP PEAK 10(6P25.2) WILD-TYPE                      172
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 10(6P25.2) MUTATED                                  3
  AMP PEAK 10(6P25.2) WILD-TYPE                                3
D10V8, multiclass
                                  clus
vv                                 AMP PEAK 10(6P25.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 131
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 AMP PEAK 10(6P25.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   172
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(6P25.2) MUTATED   119   7   1   6
  AMP PEAK 10(6P25.2) WILD-TYPE 155   7   0  10
D10V9, multiclass
    clus
vv   AMP PEAK 10(6P25.2) MUTATED AMP PEAK 10(6P25.2) WILD-TYPE
  R0                         119                           155
  R1                           7                             7
  R2                           1                             0
  RX                           6                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(6P25.2) MUTATED                                  0    64
  AMP PEAK 10(6P25.2) WILD-TYPE                                1    77
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6P25.2) MUTATED                           7    59
  AMP PEAK 10(6P25.2) WILD-TYPE                         8    86
D10V10, multiclass
                                  clus
vv                                 AMP PEAK 10(6P25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     64
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     59
                                  clus
vv                                 AMP PEAK 10(6P25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       77
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P25.2) MUTATED     4 123
  AMP PEAK 10(6P25.2) WILD-TYPE   4 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P25.2) MUTATED      4  123
  AMP PEAK 10(6P25.2) WILD-TYPE    4  164
                        clus
vv                       AMP PEAK 10(6P25.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         123
                        clus
vv                       AMP PEAK 10(6P25.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           164
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(6P21.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(6P21.1) MUTATED    80  41
  AMP PEAK 11(6P21.1) WILD-TYPE 120  51
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                          121                           171 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                           41                            51 
$`AMP PEAK 11(6P21.1) MUTATED`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z 
        7.10        10.78        27.52        27.52        23.34         1.12 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84         0.26        22.36        14.60        12.72 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC 
       13.45         0.66         0.39         4.24         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       37.78        83.57       113.00         7.33         2.60        21.76 
TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       51.29        66.31         6.71        12.95        45.11        49.15 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A3A8 TCGA-DD-A3A9 
       55.69         5.62        19.76       102.74         0.36        30.61 
TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73E 
       30.15        39.78        29.56        80.75        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB 
       27.72       100.96        13.48         0.53        65.75        59.18 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP 
       12.53        63.48        12.00        53.19        60.10        13.15 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADN 
        5.62        33.83        30.58         3.78        20.91        17.33 
TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 
        3.02         5.29         9.86         9.86         8.52        12.56 
TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       12.69        15.65        35.08        72.26        59.93        61.38 
TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XO 
       58.78        49.48        47.70        13.35         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.41         0.20         0.20        11.74        10.98         0.62 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S 
       22.85        32.45        27.88         6.38         0.39         1.22 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC 
       53.79        58.49        22.13        19.23        20.42         7.76 
TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-HP-A5N0 TCGA-KR-A7K2 TCGA-KR-A7K8 
       11.80         9.17         0.89        37.71        11.84        24.36 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V 
       12.72        18.38        12.85        20.71        16.37         4.44 
TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       21.04        15.52        24.13        14.96        17.29        14.40 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CD 
       15.98         7.04         8.32         0.99        13.55        45.57 
TCGA-ZS-A9CF 
       74.24 

$`AMP PEAK 11(6P21.1) WILD-TYPE`
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       10.59         0.66        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       46.78         2.99        25.32        69.57         5.03         9.50 
TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT 
        7.46         4.80         0.07         2.86         3.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A1E9 
        0.10         0.07        79.73        53.33         0.46        90.71 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       79.40        19.79        75.65         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       20.12       107.11        13.78        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       30.97        26.83        30.51        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        78.84        10.98         9.30         7.56 
TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL 
       11.41        55.40        15.42         6.41         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       58.16        14.33        48.49        40.77        38.04         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        34.09        22.09        31.53 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       29.26        13.97        28.41        25.08        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        0.39         3.95        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA 
        9.67         9.63         9.47         4.64        11.31        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAVP TCGA-DD-AAVQ 
       12.16        15.45        16.37        15.65        79.07        79.10 
TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A4XI 
       61.87        56.48        55.86        54.05        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       15.85        13.91         0.23         0.20         0.20        13.15 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        18.74        19.99         9.96        11.93        14.40 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10         8.12         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       60.36        51.06        28.27        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM 
       25.64         5.92        19.53        14.70        11.97        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       12.03         5.98         1.84        11.24         8.55         9.70 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF 
        2.14         3.02         1.02         2.20         2.66        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06         4.01         2.14        13.38         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 
        9.57        16.67        10.85        58.88        21.01         2.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
       19.04        15.39         1.71         4.57         1.02         4.01 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       12.99        35.05         8.22 

  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                       113.00                        108.76 
  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE 
                        14.96                         14.33 
[1] "0.1 - 113.0 (15.0)" "0.0 - 108.8 (14.3)"
[1] "hr=" "1"  
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 11(6P21.1) MUTATED        60       31         2         26
  AMP PEAK 11(6P21.1) WILD-TYPE      86       41         0         26
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 11(6P21.1) MUTATED            3          1        2         0
  AMP PEAK 11(6P21.1) WILD-TYPE          4          6        0         1
                               vv
clus                            STAGE IVB
  AMP PEAK 11(6P21.1) MUTATED           1
  AMP PEAK 11(6P21.1) WILD-TYPE         1
D11V3, multiclass
            clus
vv           AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  STAGE I                             60                            86
  STAGE II                            31                            41
  STAGE III                            2                             0
  STAGE IIIA                          26                            26
  STAGE IIIB                           3                             4
  STAGE IIIC                           1                             6
  STAGE IV                             2                             0
  STAGE IVA                            0                             1
  STAGE IVB                            1                             1
[1] 9 2
[1] 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(6P21.1) MUTATED      60 34 32  5
  AMP PEAK 11(6P21.1) WILD-TYPE    95 44 32  7
D11V4, multiclass
       clus
vv      AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  T0+T1                          60                            95
  T2                             34                            44
  T3                             32                            32
  T4                              5                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED    95   0
  AMP PEAK 11(6P21.1) WILD-TYPE 127   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED     95    0
  AMP PEAK 11(6P21.1) WILD-TYPE  127    3
   clus
vv  AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  0                          95                           127
  1                           0                             3
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 11(6P21.1) MUTATED   103   3  27
  AMP PEAK 11(6P21.1) WILD-TYPE 135   1  42
D11V6, multiclass
    clus
vv   AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  M0                         103                           135
  M1                           3                             1
  MX                          27                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED    47  86
  AMP PEAK 11(6P21.1) WILD-TYPE  53 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED     47   86
  AMP PEAK 11(6P21.1) WILD-TYPE   53  125
        clus
vv       AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  FEMALE                          47                            53
  MALE                            86                           125
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 11(6P21.1) MUTATED                         0
  AMP PEAK 11(6P21.1) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 11(6P21.1) MUTATED                        129
  AMP PEAK 11(6P21.1) WILD-TYPE                      174
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 11(6P21.1) MUTATED                                  4
  AMP PEAK 11(6P21.1) WILD-TYPE                                2
D11V8, multiclass
                                  clus
vv                                 AMP PEAK 11(6P21.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 129
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           4
                                  clus
vv                                 AMP PEAK 11(6P21.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   174
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(6P21.1) MUTATED   119   7   1   6
  AMP PEAK 11(6P21.1) WILD-TYPE 155   7   0  10
D11V9, multiclass
    clus
vv   AMP PEAK 11(6P21.1) MUTATED AMP PEAK 11(6P21.1) WILD-TYPE
  R0                         119                           155
  R1                           7                             7
  R2                           1                             0
  RX                           6                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(6P21.1) MUTATED                                  0    59
  AMP PEAK 11(6P21.1) WILD-TYPE                                1    82
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(6P21.1) MUTATED                           7    62
  AMP PEAK 11(6P21.1) WILD-TYPE                         8    83
D11V10, multiclass
                                  clus
vv                                 AMP PEAK 11(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     59
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     62
                                  clus
vv                                 AMP PEAK 11(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       82
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                               cls
clus                              0   1
  AMP PEAK 11(6P21.1) MUTATED     4 119
  AMP PEAK 11(6P21.1) WILD-TYPE   4 168
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(6P21.1) MUTATED      4  119
  AMP PEAK 11(6P21.1) WILD-TYPE    4  168
                        clus
vv                       AMP PEAK 11(6P21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         119
                        clus
vv                       AMP PEAK 11(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           168
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(6Q12) MUTATION ANALYSIS
D12V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 12(6Q12) MUTATED    52  28
  AMP PEAK 12(6Q12) WILD-TYPE 148  64
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         80                         212 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                         28                          64 
$`AMP PEAK 12(6Q12) MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       10.78        37.32        27.52        13.84         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3MB 
       14.60         7.46        13.45         0.66         4.24         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        37.78        83.57       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39Y 
       21.76         6.71        12.95        49.15        29.16         5.62 
TCGA-DD-A39Z TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       19.76       102.74        13.78         0.36        30.61        33.14 
TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73E TCGA-DD-A73G 
       30.15        39.78        29.56        80.75         1.45       100.96 
TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AAD3 TCGA-DD-AADF 
       13.48        59.18        12.53        60.10        33.83         3.78 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AAE0 TCGA-DD-AAE3 
       20.91        17.33         3.02         5.29         9.86         9.86 
TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAW2 TCGA-DD-AAW3 
       15.65        35.08        59.93        61.38        49.48        47.70 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
       13.35         0.20         0.20        10.98         0.62        22.85 
TCGA-FV-A3I0 TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A6UC TCGA-G3-AAV1 
       27.88        53.79        22.13        19.23         7.76        11.80 
TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-O8-A75V TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       11.84        12.72         4.44        15.52        24.13        14.96 
TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-YA-A8S7 
       14.40        15.98         7.04         8.32         0.99        13.55 
TCGA-ZS-A9CD TCGA-ZS-A9CF 
       45.57        74.24 

$`AMP PEAK 12(6Q12) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BD-A3ER 
       69.57         5.03        44.42         9.50        12.72         4.80 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         0.39         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
        0.07        79.73        53.33         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EI 
       79.40        66.31        19.79        75.65        45.11         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        13.64        21.14        55.69        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4ND 
       70.06        17.59        20.12       107.11        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       30.97        26.83        30.51        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
       10.98        27.72         0.53        11.41        65.75        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        53.19         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        1.91        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       34.09        22.09        31.53        30.58        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP 
       28.41        25.08        24.00        24.13         0.39         3.95 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 
       57.27         7.10         8.28         6.67         9.67         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.47         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP 
       14.79        12.16        15.45        16.37        15.65        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       79.10        72.26        61.87        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       54.05        13.41        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
        0.20         0.20         0.20        13.15        13.41         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        23.97        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.53        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        13.38        24.36         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
       16.37        21.01         2.04        21.04        19.04        15.39 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-ZP-A9CV 
       17.29         1.71         4.57         1.02         4.01         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       35.05         8.22 

  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                       0.10                        0.03 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                     113.00                      108.76 
  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE 
                     14.780                      14.365 
[1] "0.1 - 113.0 (14.8)" "0.0 - 108.8 (14.4)"
[1] "hr=" "1"  
D12V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(6Q12) MUTATED        35       21         2         18          4
  AMP PEAK 12(6Q12) WILD-TYPE     111       51         0         34          3
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(6Q12) MUTATED            4        1         0         1
  AMP PEAK 12(6Q12) WILD-TYPE          3        1         1         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  STAGE I                           35                         111
  STAGE II                          21                          51
  STAGE III                          2                           0
  STAGE IIIA                        18                          34
  STAGE IIIB                         4                           3
  STAGE IIIC                         4                           3
  STAGE IV                           1                           1
  STAGE IVA                          0                           1
  STAGE IVB                          1                           1
[1] 9 2
[1] 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(6Q12) MUTATED      36  23  25   5
  AMP PEAK 12(6Q12) WILD-TYPE   119  55  39   7
D12V4, multiclass
       clus
vv      AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  T0+T1                        36                         119
  T2                           23                          55
  T3                           25                          39
  T4                            5                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    63   2
  AMP PEAK 12(6Q12) WILD-TYPE 159   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     63    2
  AMP PEAK 12(6Q12) WILD-TYPE  159    1
   clus
vv  AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  0                        63                         159
  1                         2                           1
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 12(6Q12) MUTATED    70   2  17
  AMP PEAK 12(6Q12) WILD-TYPE 168   2  52
D12V6, multiclass
    clus
vv   AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  M0                        70                         168
  M1                         2                           2
  MX                        17                          52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED    32  57
  AMP PEAK 12(6Q12) WILD-TYPE  68 154
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED     32   57
  AMP PEAK 12(6Q12) WILD-TYPE   68  154
        clus
vv       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  FEMALE                        32                          68
  MALE                          57                         154
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 12(6Q12) MUTATED                         0                       85
  AMP PEAK 12(6Q12) WILD-TYPE                       2                      218
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 12(6Q12) MUTATED                                  4
  AMP PEAK 12(6Q12) WILD-TYPE                                2
D12V8, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                85
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         4
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 218
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
[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"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 12(6Q12) MUTATED    78   6   1   4
  AMP PEAK 12(6Q12) WILD-TYPE 196   8   0  12
D12V9, multiclass
    clus
vv   AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  R0                        78                         196
  R1                         6                           8
  R2                         1                           0
  RX                         4                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(6Q12) MUTATED                                  0    38
  AMP PEAK 12(6Q12) WILD-TYPE                                1   103
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(6Q12) MUTATED                           6    42
  AMP PEAK 12(6Q12) WILD-TYPE                         9   103
D12V10, multiclass
                                  clus
vv                                 AMP PEAK 12(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   38
  BLACK OR AFRICAN AMERICAN                                6
  WHITE                                                   42
                                  clus
vv                                 AMP PEAK 12(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    103
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                    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"
D12V11, binary
                             cls
clus                            0   1
  AMP PEAK 12(6Q12) MUTATED     3  80
  AMP PEAK 12(6Q12) WILD-TYPE   5 207
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(6Q12) MUTATED      3   80
  AMP PEAK 12(6Q12) WILD-TYPE    5  207
                        clus
vv                       AMP PEAK 12(6Q12) MUTATED AMP PEAK 12(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             3                           5
  NOT HISPANIC OR LATINO                        80                         207
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(6Q12) MUTATION ANALYSIS
D13V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 13(6Q12) MUTATED    40  18
  AMP PEAK 13(6Q12) WILD-TYPE 160  74
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         58                         234 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                         18                          74 
$`AMP PEAK 13(6Q12) MUTATED`
TCGA-5C-A9VG TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BD-A3EP 
       10.78        13.84         0.26        22.36        14.60        13.45 
TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A118 
        2.86         4.24         0.10         0.13        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39Y 
        7.33         2.60        51.29        12.95        49.15         5.62 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A73G TCGA-DD-AACJ TCGA-DD-AADF TCGA-DD-AADN 
        0.36        30.61       100.96        60.10         3.78        17.33 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEG 
        3.02         3.95         9.86         9.86        12.69        15.65 
TCGA-DD-AAEK TCGA-DD-AAVW TCGA-DD-AAW2 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O5 
       35.08        61.38        49.48        13.35         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 
       18.74        11.74        10.98         0.62        22.85        27.88 
TCGA-G3-A25U TCGA-G3-A3CK TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-O8-A75V 
       53.79        19.23        11.80        11.84        12.72         4.44 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       15.52        24.13        14.96        14.40        15.98         7.04 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CD 
        8.32         0.99        13.55        45.57 

$`AMP PEAK 13(6Q12) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A5W4 
       23.34         1.12        69.57         5.03        44.42         9.50 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       12.72         7.46         4.80         0.66         0.07         0.39 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 
        3.39         3.32         0.10         0.07        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         0.46        21.76        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65         6.71        45.11         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
        9.30         7.56        10.98         1.45        27.72        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        65.75        59.18        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        53.19         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        1.91        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       33.83        34.09        22.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       13.97        28.41        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        0.39         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.67         9.63         9.47         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
       11.31        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX 
       79.07        79.10        72.26        59.93        61.87        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       58.78        55.86        54.05        47.70        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       15.85        13.91         0.23         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A3JL 
       13.15        13.41         0.20         0.20        19.99         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        14.40        32.45        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1.22        51.06        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI 
       21.53        22.13        25.64         5.92        19.53        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       11.97        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        13.38        24.36 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71        10.85        58.88        16.37        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0V 
       21.04        19.04        15.39        17.29         1.71         4.57 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        1.02         4.01         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        24.43        12.99        35.05        74.24         8.22 

  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                       0.10                        0.03 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                     113.00                      108.76 
  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE 
                     13.150                      15.435 
[1] "0.1 - 113.0 (13.1)" "0.0 - 108.8 (15.4)"
[1] "hr=" "1.1"
D13V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(6Q12) MUTATED        27       17         1         16          1
  AMP PEAK 13(6Q12) WILD-TYPE     119       55         1         36          6
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(6Q12) MUTATED            2        1         0         1
  AMP PEAK 13(6Q12) WILD-TYPE          5        1         1         1
D13V3, multiclass
            clus
vv           AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  STAGE I                           27                         119
  STAGE II                          17                          55
  STAGE III                          1                           1
  STAGE IIIA                        16                          36
  STAGE IIIB                         1                           6
  STAGE IIIC                         2                           5
  STAGE IV                           1                           1
  STAGE IVA                          0                           1
  STAGE IVB                          1                           1
[1] 9 2
[1] 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(6Q12) MUTATED      27  17  19   4
  AMP PEAK 13(6Q12) WILD-TYPE   128  61  45   8
D13V4, multiclass
       clus
vv      AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  T0+T1                        27                         128
  T2                           17                          61
  T3                           19                          45
  T4                            4                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED    47   0
  AMP PEAK 13(6Q12) WILD-TYPE 175   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     47    0
  AMP PEAK 13(6Q12) WILD-TYPE  175    3
   clus
vv  AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  0                        47                         175
  1                         0                           3
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 13(6Q12) MUTATED    51   2  14
  AMP PEAK 13(6Q12) WILD-TYPE 187   2  55
D13V6, multiclass
    clus
vv   AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  M0                        51                         187
  M1                         2                           2
  MX                        14                          55
[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"
D13V7, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED    24  43
  AMP PEAK 13(6Q12) WILD-TYPE  76 168
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED     24   43
  AMP PEAK 13(6Q12) WILD-TYPE   76  168
        clus
vv       AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  FEMALE                        24                          76
  MALE                          43                         168
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 13(6Q12) MUTATED                         0                       64
  AMP PEAK 13(6Q12) WILD-TYPE                       2                      239
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 13(6Q12) MUTATED                                  3
  AMP PEAK 13(6Q12) WILD-TYPE                                3
D13V8, multiclass
                                  clus
vv                                 AMP PEAK 13(6Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                64
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         3
                                  clus
vv                                 AMP PEAK 13(6Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 239
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
[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"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 13(6Q12) MUTATED    60   3   1   3
  AMP PEAK 13(6Q12) WILD-TYPE 214  11   0  13
D13V9, multiclass
    clus
vv   AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  R0                        60                         214
  R1                         3                          11
  R2                         1                           0
  RX                         3                          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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(6Q12) MUTATED                                  0    34
  AMP PEAK 13(6Q12) WILD-TYPE                                1   107
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(6Q12) MUTATED                           5    27
  AMP PEAK 13(6Q12) WILD-TYPE                        10   118
D13V10, multiclass
                                  clus
vv                                 AMP PEAK 13(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   34
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   27
                                  clus
vv                                 AMP PEAK 13(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    107
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                             cls
clus                            0   1
  AMP PEAK 13(6Q12) MUTATED     3  60
  AMP PEAK 13(6Q12) WILD-TYPE   5 227
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(6Q12) MUTATED      3   60
  AMP PEAK 13(6Q12) WILD-TYPE    5  227
                        clus
vv                       AMP PEAK 13(6Q12) MUTATED AMP PEAK 13(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             3                           5
  NOT HISPANIC OR LATINO                        60                         227
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(7Q31.2) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(7Q31.2) MUTATED    59  31
  AMP PEAK 14(7Q31.2) WILD-TYPE 141  61
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                           90                           202 
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                           31                            61 
$`AMP PEAK 14(7Q31.2) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A3KF 
       10.78        10.59        37.32        10.13        27.52         0.26 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 
        9.50        14.60        13.45         4.80         0.66         2.86 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        0.10         0.10       113.00        51.29        90.71        19.79 
TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 
        6.71        29.16        21.14         5.62        19.76        70.06 
TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73C 
       33.14        26.83        39.78        12.26        78.84         7.56 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE 
        1.45       100.96        11.41        65.75        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AADD TCGA-DD-AADL 
       12.00        53.19        13.15        48.49        28.41        20.91 
TCGA-DD-AADM TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 
        0.39         7.10         6.67         9.47         9.86         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-DD-AAW3 
       12.69        14.79        12.16        56.48        49.48        47.70 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       13.41         0.23         0.20        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25T 
        9.96        22.85         8.12         6.38        60.36        51.06 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL 
       28.27        58.49        14.86        22.13        19.53        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K8 
       17.10         7.76        11.80         2.14        11.84        24.36 
TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7S9 
       12.72        16.67        18.38        58.88        16.37        21.04 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
        1.71         8.32         0.99         4.01        13.55         0.69 

$`AMP PEAK 14(7Q31.2) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T 
        7.10         0.66        48.99        27.91        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-CC-5258 
       44.42        13.84        22.36        12.72         7.46         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC 
        0.39         3.39         4.24         3.32         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF 
        0.46        21.76        79.40        66.31        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X 
       45.11        49.15         6.02        18.35        13.64        55.69 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81         7.66        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        32.52        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        30.51        56.25        29.56        73.81       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F 
        0.30        80.75        10.98         9.30        10.98        27.72 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACH 
       13.48         0.53        59.18        55.40        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACU 
       60.10         0.30         1.91        58.16        14.33        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       33.83        34.09        22.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADN 
       13.97         3.78        25.08        24.00        24.13        17.33 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADY 
        3.02         3.95         5.29        57.27         8.28         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAED 
        9.86         9.63         8.52        12.56        11.31        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.26        59.93        61.87        61.38        58.78        55.86 
TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       54.05        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20         0.20        13.15        13.41         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
        0.20        18.74        10.98        11.93        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88         0.13         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH 
        0.39         1.22        53.79        30.74        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 
        5.92        19.23        14.70        11.97        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06         4.01         2.14        13.38         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF 
        9.57        12.85        20.71        10.85         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
        2.04        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       17.29        14.40        15.98         7.04         4.57         1.02 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                       113.00                        108.76 
  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE 
                       13.430                        15.175 
[1] "0.1 - 113.0 (13.4)" "0.0 - 108.8 (15.2)"
[1] "hr=" "1.2"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 14(7Q31.2) MUTATED        44       23         0         19
  AMP PEAK 14(7Q31.2) WILD-TYPE     102       49         2         33
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 14(7Q31.2) MUTATED            2          5        1         0
  AMP PEAK 14(7Q31.2) WILD-TYPE          5          2        1         1
                               vv
clus                            STAGE IVB
  AMP PEAK 14(7Q31.2) MUTATED           0
  AMP PEAK 14(7Q31.2) WILD-TYPE         2
D14V3, multiclass
            clus
vv           AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  STAGE I                             44                           102
  STAGE II                            23                            49
  STAGE III                            0                             2
  STAGE IIIA                          19                            33
  STAGE IIIB                           2                             5
  STAGE IIIC                           5                             2
  STAGE IV                             1                             1
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] 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(7Q31.2) MUTATED      46  27  22   4
  AMP PEAK 14(7Q31.2) WILD-TYPE   109  51  42   8
D14V4, multiclass
       clus
vv      AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  T0+T1                          46                           109
  T2                             27                            51
  T3                             22                            42
  T4                              4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED    67   2
  AMP PEAK 14(7Q31.2) WILD-TYPE 155   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED     67    2
  AMP PEAK 14(7Q31.2) WILD-TYPE  155    1
   clus
vv  AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  0                          67                           155
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 14(7Q31.2) MUTATED    78   1  20
  AMP PEAK 14(7Q31.2) WILD-TYPE 160   3  49
D14V6, multiclass
    clus
vv   AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  M0                          78                           160
  M1                           1                             3
  MX                          20                            49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED    30  69
  AMP PEAK 14(7Q31.2) WILD-TYPE  70 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED     30   69
  AMP PEAK 14(7Q31.2) WILD-TYPE   70  142
        clus
vv       AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  FEMALE                          30                            70
  MALE                            69                           142
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 14(7Q31.2) MUTATED                         0
  AMP PEAK 14(7Q31.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 14(7Q31.2) MUTATED                         98
  AMP PEAK 14(7Q31.2) WILD-TYPE                      205
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 14(7Q31.2) MUTATED                                  1
  AMP PEAK 14(7Q31.2) WILD-TYPE                                5
D14V8, multiclass
                                  clus
vv                                 AMP PEAK 14(7Q31.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  98
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 14(7Q31.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   205
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             5
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(7Q31.2) MUTATED    86   6   0   5
  AMP PEAK 14(7Q31.2) WILD-TYPE 188   8   1  11
D14V9, multiclass
    clus
vv   AMP PEAK 14(7Q31.2) MUTATED AMP PEAK 14(7Q31.2) WILD-TYPE
  R0                          86                           188
  R1                           6                             8
  R2                           0                             1
  RX                           5                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(7Q31.2) MUTATED                                  1    40
  AMP PEAK 14(7Q31.2) WILD-TYPE                                0   101
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(7Q31.2) MUTATED                           4    52
  AMP PEAK 14(7Q31.2) WILD-TYPE                        11    93
D14V10, multiclass
                                  clus
vv                                 AMP PEAK 14(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     40
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     52
                                  clus
vv                                 AMP PEAK 14(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                      101
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                       93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q31.2) MUTATED     4  91
  AMP PEAK 14(7Q31.2) WILD-TYPE   4 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q31.2) MUTATED      4   91
  AMP PEAK 14(7Q31.2) WILD-TYPE    4  196
                        clus
vv                       AMP PEAK 14(7Q31.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          91
                        clus
vv                       AMP PEAK 14(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           196
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(8Q13.3) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(8Q13.3) MUTATED   115  48
  AMP PEAK 15(8Q13.3) WILD-TYPE  85  44
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                          163                           129 
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                           48                            44 
$`AMP PEAK 15(8Q13.3) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       10.78        10.59        48.99        46.78        27.52         2.99 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       44.42         0.26        14.60         4.80         0.66         0.07 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 
        3.32         0.10         0.10         0.13        79.73        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC 
      113.00         7.33         2.60        21.76        90.71        19.79 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V 
        6.71        12.95        45.11         6.02        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A8 TCGA-DD-A4ND 
        5.62        19.76         7.66        17.59         0.36        73.38 
TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO 
       30.97        26.83        30.51        39.78        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AAC8 
       12.26         0.30        80.75        10.98       100.96         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG 
       11.41        65.75        59.18        12.53        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
        6.41        53.19        60.10        58.16        13.15        14.33 
TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
        5.62        18.54        21.63        34.09        22.09        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       29.26        13.97        28.41        25.08        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        17.33         3.02         3.95         5.29        57.27 
TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 
        8.28         9.86         9.63         9.86         4.64        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVQ 
       12.69        12.16        15.45        15.65        35.08        79.10 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y 
       54.05        49.48        47.70        13.41        13.35         0.23 
TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        18.74        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 
        9.96        11.93        22.85        14.40        23.97         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        6.38        60.36         0.39        51.06        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CJ TCGA-G3-A5SI 
       58.49        21.53        22.13        25.64        19.53        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       11.97        20.42        12.03         5.98         1.84        11.24 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-K7-A6G5 
       11.80         9.70         9.17         2.14         2.66         4.01 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.84        13.38        24.36         4.27         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF 
       12.85        20.71        10.85        16.37         4.44        19.04 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       15.39        24.13        14.96         1.71        15.98         8.32 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D4 TCGA-ZS-A9CD 
        0.99         4.01        13.55         4.67        12.99        45.57 
TCGA-ZS-A9CG 
        8.22 

$`AMP PEAK 15(8Q13.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
        7.10         0.66        27.91        37.32        10.13        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 
       25.32        23.34         1.12        69.57         5.03        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 
       22.36         9.50        12.72         7.46        13.45         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 
        0.39         3.39         4.24         0.07        37.78        83.57 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH 
        0.46        51.29        79.40        66.31        75.65        49.15 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 
       29.16        18.35        55.69        25.81        70.06        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       30.15        56.25       108.76        78.84        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AACC TCGA-DD-AACE 
        7.56         1.45        27.72        13.48        55.40        63.48 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
        0.30         1.91        48.49        40.77        38.04         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADS 
        4.50        33.83        31.53         3.78        24.00         7.10 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEA 
        6.67         9.67         9.47         8.52        12.56        14.79 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-ED-A4XI TCGA-ED-A5KG 
       16.37        15.65        79.07        72.26        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.91         0.20         0.20         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        0.20         0.20        19.99        32.45        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Y 
        0.13         0.03         0.33         1.22        53.79        14.86 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-AAV0 TCGA-G3-AAV4 
        5.92        19.23        17.10         7.76         8.55         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        3.02         1.02         2.20        37.71        20.75        17.06 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-NI-A4U2 TCGA-PD-A5DF 
        2.14        12.72         5.92        18.38        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MF 
        2.04        21.04        15.52        17.29        14.40         7.04 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
        4.57         1.02        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       24.43        35.05        74.24 

  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                       113.00                        108.76 
  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE 
                        13.97                         15.52 
[1] "0.1 - 113.0 (14.0)" "0.0 - 108.8 (15.5)"
[1] "hr=" "1.1"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 15(8Q13.3) MUTATED        82       45         0         34
  AMP PEAK 15(8Q13.3) WILD-TYPE      64       27         2         18
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 15(8Q13.3) MUTATED            3          2        2         1
  AMP PEAK 15(8Q13.3) WILD-TYPE          4          5        0         0
                               vv
clus                            STAGE IVB
  AMP PEAK 15(8Q13.3) MUTATED           0
  AMP PEAK 15(8Q13.3) WILD-TYPE         2
D15V3, multiclass
            clus
vv           AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  STAGE I                             82                            64
  STAGE II                            45                            27
  STAGE III                            0                             2
  STAGE IIIA                          34                            18
  STAGE IIIB                           3                             4
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            1                             0
  STAGE IVB                            0                             2
[1] 9 2
[1] 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(8Q13.3) MUTATED      85 48 39  4
  AMP PEAK 15(8Q13.3) WILD-TYPE    70 30 25  8
D15V4, multiclass
       clus
vv      AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  T0+T1                          85                            70
  T2                             48                            30
  T3                             39                            25
  T4                              4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED   131   1
  AMP PEAK 15(8Q13.3) WILD-TYPE  91   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED    131    1
  AMP PEAK 15(8Q13.3) WILD-TYPE   91    2
   clus
vv  AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  0                         131                            91
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 15(8Q13.3) MUTATED   139   2  36
  AMP PEAK 15(8Q13.3) WILD-TYPE  99   2  33
D15V6, multiclass
    clus
vv   AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  M0                         139                            99
  M1                           2                             2
  MX                          36                            33
[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"
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED    42 135
  AMP PEAK 15(8Q13.3) WILD-TYPE  58  76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED     42  135
  AMP PEAK 15(8Q13.3) WILD-TYPE   58   76
        clus
vv       AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  FEMALE                          42                            58
  MALE                           135                            76
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 15(8Q13.3) MUTATED                         1
  AMP PEAK 15(8Q13.3) WILD-TYPE                       1
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 15(8Q13.3) MUTATED                        174
  AMP PEAK 15(8Q13.3) WILD-TYPE                      129
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 15(8Q13.3) MUTATED                                  2
  AMP PEAK 15(8Q13.3) WILD-TYPE                                4
D15V8, multiclass
                                  clus
vv                                 AMP PEAK 15(8Q13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 174
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 AMP PEAK 15(8Q13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   129
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 15(8Q13.3) MUTATED   156   9   1   8
  AMP PEAK 15(8Q13.3) WILD-TYPE 118   5   0   8
D15V9, multiclass
    clus
vv   AMP PEAK 15(8Q13.3) MUTATED AMP PEAK 15(8Q13.3) WILD-TYPE
  R0                         156                           118
  R1                           9                             5
  R2                           1                             0
  RX                           8                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(8Q13.3) MUTATED                                  1    88
  AMP PEAK 15(8Q13.3) WILD-TYPE                                0    53
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8Q13.3) MUTATED                           9    73
  AMP PEAK 15(8Q13.3) WILD-TYPE                         6    72
D15V10, multiclass
                                  clus
vv                                 AMP PEAK 15(8Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     88
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     73
                                  clus
vv                                 AMP PEAK 15(8Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       53
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
                               cls
clus                              0   1
  AMP PEAK 15(8Q13.3) MUTATED     7 161
  AMP PEAK 15(8Q13.3) WILD-TYPE   1 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8Q13.3) MUTATED      7  161
  AMP PEAK 15(8Q13.3) WILD-TYPE    1  126
                        clus
vv                       AMP PEAK 15(8Q13.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         161
                        clus
vv                       AMP PEAK 15(8Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           126
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(8Q24.21) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(8Q24.21) MUTATED   131  52
  AMP PEAK 16(8Q24.21) WILD-TYPE  69  40
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                           183                            109 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                            52                             40 
$`AMP PEAK 16(8Q24.21) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       10.78        10.59        48.99        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 
        2.99         0.26        14.60        13.45         4.80         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.39         3.39         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        79.73        53.33       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       21.76        90.71        19.79         6.71        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
        6.02        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NF 
        7.66        17.59        13.78         0.36        73.38        30.97 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       26.83        30.51        39.78        29.56        73.81        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AAC8 
        0.30        80.75        10.98        10.98       100.96         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG 
       11.41        65.75        59.18        12.53        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACS 
        6.41        53.19        60.10        58.16        13.15        48.49 
TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
       38.04         5.62         4.50        18.54        21.63        34.09 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI 
       22.09        30.58        29.26        13.97        28.41        25.08 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       24.13        20.91         0.39        17.33         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 
        5.29        57.27         8.28         9.86         9.63         9.86 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        12.56        11.31        12.69        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        15.65        15.65        35.08        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y 
       54.05        49.48        47.70        13.41        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15        13.41         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        23.97        27.88         8.12         6.38 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CJ TCGA-G3-A5SI 
       58.49        21.53        22.13        25.64        19.53        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV1 
       11.97        20.42        12.03         5.98        11.24        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A6G5 
        9.70         9.17         2.14         3.02         2.66         4.01 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.84        13.38        24.36         4.27         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF 
       12.85        20.71        10.85        16.37         4.44        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        24.13        14.96        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
       15.98         8.32         0.99         4.01        13.55         4.67 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        45.57         8.22 

$`AMP PEAK 16(8Q24.21) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10X 
        7.10         0.66        27.91        37.32        10.13        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5260 
       22.36         9.50        12.72         7.46         0.66         2.86 
TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
        4.24        37.78        83.57         0.46        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A3A0 
       66.31        75.65        49.15        29.16        18.35        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA 
       70.06        20.12       102.74       107.11        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NV TCGA-DD-A73B 
       32.52        30.15        56.25       108.76        78.84         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AACC TCGA-DD-AACE 
        7.56         1.45        27.72        13.48        55.40        63.48 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AAD3 
        0.30         1.91        14.33        40.77         5.59        33.83 
TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY 
       31.53         3.78        24.00         7.10         6.67         9.67 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAEA TCGA-DD-AAVP TCGA-ED-A4XI TCGA-ED-A5KG 
        9.47         8.52        14.79        79.07        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A26S TCGA-FV-A23B 
       13.91         0.20         0.20         0.20        19.99        32.45 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Y 
       19.10         0.13         0.03         0.33         1.22        14.86 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-G3-AAV0 
        5.92        19.23        17.10         7.76         1.84         8.55 
TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        0.89         1.02         2.20        37.71        20.75        17.06 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-NI-A4U2 TCGA-PD-A5DF 
        2.14        12.72         5.92        18.38        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-UB-A7MB TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
        2.04        21.04        17.29         7.04         4.57         1.02 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       25.71        23.21        23.57         0.69        24.43        35.05 
TCGA-ZS-A9CF 
       74.24 

  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                        113.00                         108.76 
  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE 
                         13.78                          17.06 
[1] "0.1 - 113.0 (13.8)" "0.0 - 108.8 (17.1)"
[1] "hr=" "1.2"
D16V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 16(8Q24.21) MUTATED        94       50         0         37
  AMP PEAK 16(8Q24.21) WILD-TYPE      52       22         2         15
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 16(8Q24.21) MUTATED            3          3        2         1
  AMP PEAK 16(8Q24.21) WILD-TYPE          4          4        0         0
                                vv
clus                             STAGE IVB
  AMP PEAK 16(8Q24.21) MUTATED           0
  AMP PEAK 16(8Q24.21) WILD-TYPE         2
D16V3, multiclass
            clus
vv           AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  STAGE I                              94                             52
  STAGE II                             50                             22
  STAGE III                             0                              2
  STAGE IIIA                           37                             15
  STAGE IIIB                            3                              4
  STAGE IIIC                            3                              4
  STAGE IV                              2                              0
  STAGE IVA                             1                              0
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(8Q24.21) MUTATED      97 53 42  6
  AMP PEAK 16(8Q24.21) WILD-TYPE    58 25 22  6
D16V4, multiclass
       clus
vv      AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  T0+T1                           97                             58
  T2                              53                             25
  T3                              42                             22
  T4                               6                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED   152   1
  AMP PEAK 16(8Q24.21) WILD-TYPE  70   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED    152    1
  AMP PEAK 16(8Q24.21) WILD-TYPE   70    2
   clus
vv  AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  0                          152                             70
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 16(8Q24.21) MUTATED   161   2  36
  AMP PEAK 16(8Q24.21) WILD-TYPE  77   2  33
D16V6, multiclass
    clus
vv   AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  M0                          161                             77
  M1                            2                              2
  MX                           36                             33
[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"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED    49 150
  AMP PEAK 16(8Q24.21) WILD-TYPE  51  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED     49  150
  AMP PEAK 16(8Q24.21) WILD-TYPE   51   61
        clus
vv       AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  FEMALE                           49                             51
  MALE                            150                             61
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                         1
  AMP PEAK 16(8Q24.21) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 16(8Q24.21) MUTATED                        194
  AMP PEAK 16(8Q24.21) WILD-TYPE                      109
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 16(8Q24.21) MUTATED                                  4
  AMP PEAK 16(8Q24.21) WILD-TYPE                                2
D16V8, multiclass
                                  clus
vv                                 AMP PEAK 16(8Q24.21) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  194
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 AMP PEAK 16(8Q24.21) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    109
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              2
[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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(8Q24.21) MUTATED   176  10   1   8
  AMP PEAK 16(8Q24.21) WILD-TYPE  98   4   0   8
D16V9, multiclass
    clus
vv   AMP PEAK 16(8Q24.21) MUTATED AMP PEAK 16(8Q24.21) WILD-TYPE
  R0                          176                             98
  R1                           10                              4
  R2                            1                              0
  RX                            8                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(8Q24.21) MUTATED                                  1   106
  AMP PEAK 16(8Q24.21) WILD-TYPE                                0    35
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(8Q24.21) MUTATED                           9    76
  AMP PEAK 16(8Q24.21) WILD-TYPE                         6    69
D16V10, multiclass
                                  clus
vv                                 AMP PEAK 16(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                     106
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      76
                                  clus
vv                                 AMP PEAK 16(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        35
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        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"
D16V11, binary
                                cls
clus                               0   1
  AMP PEAK 16(8Q24.21) MUTATED     7 183
  AMP PEAK 16(8Q24.21) WILD-TYPE   1 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8Q24.21) MUTATED      7  183
  AMP PEAK 16(8Q24.21) WILD-TYPE    1  104
                        clus
vv                       AMP PEAK 16(8Q24.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          183
                        clus
vv                       AMP PEAK 16(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            104
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(9Q34.2) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(9Q34.2) MUTATED    19  13
  AMP PEAK 17(9Q34.2) WILD-TYPE 181  79
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           32                           260 
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                           13                            79 
$`AMP PEAK 17(9Q34.2) MUTATED`
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 
       27.52        23.34         7.46         0.66         0.39         4.24 
TCGA-DD-A1EG TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NV TCGA-DD-A73G 
       45.11        25.81       102.74       107.11        78.84       100.96 
TCGA-DD-AAD6 TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAVZ 
       22.09        24.00         3.02         9.86         9.47        55.86 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A495 
        0.23        13.41        10.98        22.85        23.97         0.03 
TCGA-FV-A4ZP TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-KR-A7K2 TCGA-KR-A7K8 
       60.36        53.79        22.13         1.84        11.84        24.36 
TCGA-WQ-A9G7 TCGA-ZS-A9CF 
        0.99        74.24 

$`AMP PEAK 17(9Q34.2) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        46.78        27.52         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3EP TCGA-BD-A3ER 
       22.36         9.50        14.60        12.72        13.45         4.80 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.07         2.86         3.39         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        55.69         5.62        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       17.59        20.12        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        27.72        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       59.18        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        60.10         0.30         1.91        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       13.15        14.33        48.49        40.77        38.04         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        33.83        34.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       31.53        30.58        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       25.08        24.13        20.91         0.39        17.33         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.63         9.86         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       12.69        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        35.08        79.07        79.10        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.87        61.38        56.48        58.78        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
        0.20         0.20         0.20         0.20        13.15         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
        8.12         6.38         0.13         0.33         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       20.42        17.10         7.76        12.03         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
        8.55        11.80         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC 
       17.06         4.01         2.14        13.38        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        4.27         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         1.02         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       35.05         8.22 

  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                       107.11                        113.00 
  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE 
                       22.490                        14.365 
[1] "0.0 - 107.1 (22.5)" "0.1 - 113.0 (14.4)"
[1] "hr=" "1"  
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 17(9Q34.2) MUTATED        13        5         1         12
  AMP PEAK 17(9Q34.2) WILD-TYPE     133       67         1         40
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 17(9Q34.2) MUTATED            1          1        1         1
  AMP PEAK 17(9Q34.2) WILD-TYPE          6          6        1         0
                               vv
clus                            STAGE IVB
  AMP PEAK 17(9Q34.2) MUTATED           0
  AMP PEAK 17(9Q34.2) WILD-TYPE         2
D17V3, multiclass
            clus
vv           AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  STAGE I                             13                           133
  STAGE II                             5                            67
  STAGE III                            1                             1
  STAGE IIIA                          12                            40
  STAGE IIIB                           1                             6
  STAGE IIIC                           1                             6
  STAGE IV                             1                             1
  STAGE IVA                            1                             0
  STAGE IVB                            0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 17(9Q34.2) MUTATED      14   6  15   3
  AMP PEAK 17(9Q34.2) WILD-TYPE   141  72  49   9
D17V4, multiclass
       clus
vv      AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  T0+T1                          14                           141
  T2                              6                            72
  T3                             15                            49
  T4                              3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED    26   1
  AMP PEAK 17(9Q34.2) WILD-TYPE 196   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED     26    1
  AMP PEAK 17(9Q34.2) WILD-TYPE  196    2
   clus
vv  AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  0                          26                           196
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 17(9Q34.2) MUTATED    29   1   8
  AMP PEAK 17(9Q34.2) WILD-TYPE 209   3  61
D17V6, multiclass
    clus
vv   AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  M0                          29                           209
  M1                           1                             3
  MX                           8                            61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED    14  24
  AMP PEAK 17(9Q34.2) WILD-TYPE  86 187
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED     14   24
  AMP PEAK 17(9Q34.2) WILD-TYPE   86  187
        clus
vv       AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  FEMALE                          14                            86
  MALE                            24                           187
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  AMP PEAK 17(9Q34.2) MUTATED                         0
  AMP PEAK 17(9Q34.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  AMP PEAK 17(9Q34.2) MUTATED                         37
  AMP PEAK 17(9Q34.2) WILD-TYPE                      266
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 17(9Q34.2) MUTATED                                  1
  AMP PEAK 17(9Q34.2) WILD-TYPE                                5
D17V8, multiclass
                                  clus
vv                                 AMP PEAK 17(9Q34.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  37
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 AMP PEAK 17(9Q34.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   266
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             5
[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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 17(9Q34.2) MUTATED    30   3   0   5
  AMP PEAK 17(9Q34.2) WILD-TYPE 244  11   1  11
D17V9, multiclass
    clus
vv   AMP PEAK 17(9Q34.2) MUTATED AMP PEAK 17(9Q34.2) WILD-TYPE
  R0                          30                           244
  R1                           3                            11
  R2                           0                             1
  RX                           5                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(9Q34.2) MUTATED                                  0    16
  AMP PEAK 17(9Q34.2) WILD-TYPE                                1   125
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(9Q34.2) MUTATED                           1    20
  AMP PEAK 17(9Q34.2) WILD-TYPE                        14   125
D17V10, multiclass
                                  clus
vv                                 AMP PEAK 17(9Q34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     16
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     20
                                  clus
vv                                 AMP PEAK 17(9Q34.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      125
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                               cls
clus                              0   1
  AMP PEAK 17(9Q34.2) MUTATED     1  35
  AMP PEAK 17(9Q34.2) WILD-TYPE   7 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.2) MUTATED      1   35
  AMP PEAK 17(9Q34.2) WILD-TYPE    7  252
                        clus
vv                       AMP PEAK 17(9Q34.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          35
                        clus
vv                       AMP PEAK 17(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           252
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(11Q13.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(11Q13.3) MUTATED    35  10
  AMP PEAK 18(11Q13.3) WILD-TYPE 165  82
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            45                            247 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            10                             82 
$`AMP PEAK 18(11Q13.3) MUTATED`
TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A3KG TCGA-BC-A69I TCGA-BD-A3EP TCGA-BD-A3ER 
       27.91        27.52        22.36        12.72        13.45         4.80 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EB 
        0.10         0.10        83.57         7.33         2.60        66.31 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NV TCGA-DD-A73E 
        5.62        25.81        73.38        29.56        78.84         1.45 
TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AAD1 TCGA-DD-AAD8 TCGA-DD-AADL TCGA-DD-AADP 
      100.96        59.18        18.54        31.53        20.91         3.95 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-ED-A66Y TCGA-ED-A82E 
        9.67         9.86         4.64        15.45         0.23        13.41 
TCGA-EP-A2KA TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A3CG 
       11.74         0.33         0.39         1.22        30.74        22.13 
TCGA-G3-A5SJ TCGA-G3-AAV0 TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K8 TCGA-LG-A6GG 
       11.97         8.55         2.20        17.06        24.36        12.72 
TCGA-RC-A7SF TCGA-UB-A7ME TCGA-WQ-A9G7 
       19.04        15.98         0.99 

$`AMP PEAK 18(11Q13.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-A10Q 
        7.10        10.78        10.59         0.66        48.99        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
        9.50        14.60         7.46         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC 
        0.39         3.39         4.24         3.32         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       79.73        37.78        53.33       113.00         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        90.71        79.40        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        39.78        56.25        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
       27.72        13.48         0.53        11.41        65.75        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        33.83        34.09        22.09        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       13.97        28.41         3.78        25.08        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        17.33         3.02         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
        8.28         6.67         9.63         9.47         9.86         8.52 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE 
       12.56        11.31        12.69        14.79        12.16        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.65        15.65        35.08        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91        13.35         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       32.45        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.13         0.03        60.36        51.06        53.79        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       19.23        14.70        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        5.98         1.84        11.24        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         2.14         3.02         1.02         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC 
       20.75         4.01         2.14        11.84        13.38         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        4.27         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        15.39        15.52        24.13        14.96        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       14.40         1.71         7.04         8.32         4.57         1.02 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.01        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                        100.96                         113.00 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                         13.41                          14.70 
[1] "0.1 - 101.0 (13.4)" "0.0 - 113.0 (14.7)"
[1] "hr=" "1.4"
D18V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 18(11Q13.3) MUTATED        30        4         0         12
  AMP PEAK 18(11Q13.3) WILD-TYPE     116       68         2         40
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(11Q13.3) MUTATED            1          0        1         0
  AMP PEAK 18(11Q13.3) WILD-TYPE          6          7        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 18(11Q13.3) MUTATED           0
  AMP PEAK 18(11Q13.3) WILD-TYPE         2
D18V3, multiclass
            clus
vv           AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  STAGE I                              30                            116
  STAGE II                              4                             68
  STAGE III                             0                              2
  STAGE IIIA                           12                             40
  STAGE IIIB                            1                              6
  STAGE IIIC                            0                              7
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(11Q13.3) MUTATED      30   4  15   1
  AMP PEAK 18(11Q13.3) WILD-TYPE   125  74  49  11
D18V4, multiclass
       clus
vv      AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  T0+T1                           30                            125
  T2                               4                             74
  T3                              15                             49
  T4                               1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    37   0
  AMP PEAK 18(11Q13.3) WILD-TYPE 185   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     37    0
  AMP PEAK 18(11Q13.3) WILD-TYPE  185    3
   clus
vv  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  0                           37                            185
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 18(11Q13.3) MUTATED    41   1   8
  AMP PEAK 18(11Q13.3) WILD-TYPE 197   3  61
D18V6, multiclass
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  M0                           41                            197
  M1                            1                              3
  MX                            8                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    19  31
  AMP PEAK 18(11Q13.3) WILD-TYPE  81 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     19   31
  AMP PEAK 18(11Q13.3) WILD-TYPE   81  180
        clus
vv       AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  FEMALE                           19                             81
  MALE                             31                            180
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                         0
  AMP PEAK 18(11Q13.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                         50
  AMP PEAK 18(11Q13.3) WILD-TYPE                      253
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 18(11Q13.3) MUTATED                                  0
  AMP PEAK 18(11Q13.3) WILD-TYPE                                6
D18V8, multiclass
                                  clus
vv                                 AMP PEAK 18(11Q13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   50
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 AMP PEAK 18(11Q13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    253
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              6
[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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(11Q13.3) MUTATED    42   5   1   2
  AMP PEAK 18(11Q13.3) WILD-TYPE 232   9   0  14
D18V9, multiclass
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  R0                           42                            232
  R1                            5                              9
  R2                            1                              0
  RX                            2                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(11Q13.3) MUTATED                                  0    22
  AMP PEAK 18(11Q13.3) WILD-TYPE                                1   119
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(11Q13.3) MUTATED                           3    23
  AMP PEAK 18(11Q13.3) WILD-TYPE                        12   122
D18V10, multiclass
                                  clus
vv                                 AMP PEAK 18(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      22
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      23
                                  clus
vv                                 AMP PEAK 18(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       119
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED     0  46
  AMP PEAK 18(11Q13.3) WILD-TYPE   8 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED      0   46
  AMP PEAK 18(11Q13.3) WILD-TYPE    8  241
                        clus
vv                       AMP PEAK 18(11Q13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           46
                        clus
vv                       AMP PEAK 18(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            241
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(13Q32.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(13Q32.3) MUTATED    35  17
  AMP PEAK 19(13Q32.3) WILD-TYPE 165  75
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            52                            240 
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                            17                             75 
$`AMP PEAK 19(13Q32.3) MUTATED`
TCGA-BC-A10W TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A8YO TCGA-BD-A3EP 
        2.99         1.12        44.42         0.26         7.46        13.45 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A11A 
        0.07         0.39         4.24         0.07        79.73         2.60 
TCGA-DD-A11C TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       21.76        45.11        29.16        13.64        55.69         5.62 
TCGA-DD-A3A7 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AAD5 TCGA-DD-AADD 
       13.78        65.75        59.18        63.48        34.09        28.41 
TCGA-DD-AADF TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 
        3.78         6.67         9.86         9.86         4.64        11.31 
TCGA-DD-AAEK TCGA-DD-AAVW TCGA-ED-A7PY TCGA-EP-A2KA TCGA-EP-A3JL TCGA-FV-A23B 
       35.08        61.38         0.20        11.74         9.96        32.45 
TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 
       27.88         0.33        12.03        11.80         2.14        11.84 
TCGA-KR-A7K8 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-UB-A7MA 
       24.36        16.37        21.01        21.04        24.13        14.96 
TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U TCGA-ZP-A9CZ 
       14.40         7.04         8.32        23.21 

$`AMP PEAK 19(13Q32.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       37.32        10.13        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
       23.34        69.57         5.03        13.84        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5262 
       14.60        12.72         4.80         0.66         2.86         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.10         0.10         0.13        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
       53.33       113.00         7.33         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 
       49.15         6.02        18.35        21.14        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACD 
      100.96        13.48         0.53        11.41        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        1.91        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       33.83        22.09        31.53        30.58        29.26        13.97 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       25.08        24.00        24.13        20.91         0.39        17.33 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        3.02         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
        9.67         9.63         9.47         8.52        12.56        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       14.79        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX 
       79.07        79.10        72.26        59.93        61.87        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20         0.20        13.15        13.41         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
        0.20        18.74        19.99        10.98         0.62        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        23.97        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.13         0.03        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       11.97        20.42        17.10         7.76         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
       11.24         8.55         9.70         9.17         0.89         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        4.01         2.14        13.38        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57        16.67        18.38        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       58.88         4.44         2.04        19.04        15.39        15.52 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       17.29         1.71        15.98         4.57         1.02         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D1 
        4.01        13.55         4.67        25.71        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        35.05        74.24         8.22 

  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                         79.73                         113.00 
  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE 
                        12.740                         15.125 
[1] "0.1 - 79.7 (12.7)"  "0.0 - 113.0 (15.1)"
[1] "hr=" "1.3"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 19(13Q32.3) MUTATED        26       12         0         12
  AMP PEAK 19(13Q32.3) WILD-TYPE     120       60         2         40
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 19(13Q32.3) MUTATED            2          3        1         0
  AMP PEAK 19(13Q32.3) WILD-TYPE          5          4        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 19(13Q32.3) MUTATED           0
  AMP PEAK 19(13Q32.3) WILD-TYPE         2
D19V3, multiclass
            clus
vv           AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  STAGE I                              26                            120
  STAGE II                             12                             60
  STAGE III                             0                              2
  STAGE IIIA                           12                             40
  STAGE IIIB                            2                              5
  STAGE IIIC                            3                              4
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(13Q32.3) MUTATED      28  13  13   4
  AMP PEAK 19(13Q32.3) WILD-TYPE   127  65  51   8
D19V4, multiclass
       clus
vv      AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  T0+T1                           28                            127
  T2                              13                             65
  T3                              13                             51
  T4                               4                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q32.3) MUTATED    42   1
  AMP PEAK 19(13Q32.3) WILD-TYPE 180   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED     42    1
  AMP PEAK 19(13Q32.3) WILD-TYPE  180    2
   clus
vv  AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  0                           42                            180
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 19(13Q32.3) MUTATED    47   1  10
  AMP PEAK 19(13Q32.3) WILD-TYPE 191   3  59
D19V6, multiclass
    clus
vv   AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  M0                           47                            191
  M1                            1                              3
  MX                           10                             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q32.3) MUTATED    25  33
  AMP PEAK 19(13Q32.3) WILD-TYPE  75 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED     25   33
  AMP PEAK 19(13Q32.3) WILD-TYPE   75  178
        clus
vv       AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  FEMALE                           25                             75
  MALE                             33                            178
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 19(13Q32.3) MUTATED                         0
  AMP PEAK 19(13Q32.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 19(13Q32.3) MUTATED                         55
  AMP PEAK 19(13Q32.3) WILD-TYPE                      248
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 19(13Q32.3) MUTATED                                  3
  AMP PEAK 19(13Q32.3) WILD-TYPE                                3
D19V8, multiclass
                                  clus
vv                                 AMP PEAK 19(13Q32.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   55
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK 19(13Q32.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    248
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              3
[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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(13Q32.3) MUTATED    48   3   0   5
  AMP PEAK 19(13Q32.3) WILD-TYPE 226  11   1  11
D19V9, multiclass
    clus
vv   AMP PEAK 19(13Q32.3) MUTATED AMP PEAK 19(13Q32.3) WILD-TYPE
  R0                           48                            226
  R1                            3                             11
  R2                            0                              1
  RX                            5                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(13Q32.3) MUTATED                                  0    28
  AMP PEAK 19(13Q32.3) WILD-TYPE                                1   113
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(13Q32.3) MUTATED                           4    24
  AMP PEAK 19(13Q32.3) WILD-TYPE                        11   121
D19V10, multiclass
                                  clus
vv                                 AMP PEAK 19(13Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      28
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      24
                                  clus
vv                                 AMP PEAK 19(13Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       113
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       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"
D19V11, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q32.3) MUTATED     2  51
  AMP PEAK 19(13Q32.3) WILD-TYPE   6 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q32.3) MUTATED      2   51
  AMP PEAK 19(13Q32.3) WILD-TYPE    6  236
                        clus
vv                       AMP PEAK 19(13Q32.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           51
                        clus
vv                       AMP PEAK 19(13Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            236
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(13Q33.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(13Q33.3) MUTATED    38  16
  AMP PEAK 20(13Q33.3) WILD-TYPE 162  76
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            54                            238 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                            16                             76 
$`AMP PEAK 20(13Q33.3) MUTATED`
TCGA-BC-A10W TCGA-BC-A217 TCGA-BC-A3KF TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5261 
        2.99        13.84         0.26        13.45         0.07         0.39 
TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EJ 
        4.24         0.07        79.73         2.60        45.11        29.16 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A7 TCGA-DD-AACA TCGA-DD-AACB 
       13.64        55.69         5.62        13.78        65.75        59.18 
TCGA-DD-AACE TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADQ TCGA-DD-AADW 
       63.48        34.09        28.41         3.78         5.29         6.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEK 
        9.86         9.63         9.86         4.64        11.31        35.08 
TCGA-DD-AAVW TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3JL 
       61.38         0.23         0.20        19.99         0.62         9.96 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 
       32.45        27.88         0.33        12.03        11.80         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 
       11.84        24.36        16.37        21.04        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZP-A9CZ 
       14.96        14.40         7.04         8.32         1.02        23.21 

$`AMP PEAK 20(13Q33.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       37.32        10.13        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG 
       23.34         1.12        69.57         5.03        44.42        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO 
        9.50        14.60        12.72         7.46         4.80         0.66 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        2.86         3.39         3.32         0.10         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        12.95        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       10.98         1.45        27.72       100.96        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       11.41        55.40        12.53        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       53.19        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       14.33        48.49        40.77        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        33.83        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       30.58        29.26        13.97        25.08        24.00        24.13 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR 
       20.91         0.39        17.33         3.02         3.95        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 
        7.10         8.28         9.67         9.47         8.52        12.56 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       12.69        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       15.65        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20         0.20        13.15        13.41         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HS 
        0.20        18.74        11.74        10.98        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        23.97        19.10         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       20.42        17.10         7.76         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        8.55         9.70         9.17         0.89         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        13.38        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB 
        4.44        21.01         2.04        19.04        15.39        17.29 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        1.71        15.98         4.57         0.99         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
        4.67        25.71        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                         79.73                         113.00 
  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE 
                        11.935                         15.435 
[1] "0.1 - 79.7 (11.9)"  "0.0 - 113.0 (15.4)"
[1] "hr=" "1.2"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 20(13Q33.3) MUTATED        29       14         0         11
  AMP PEAK 20(13Q33.3) WILD-TYPE     117       58         2         41
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 20(13Q33.3) MUTATED            1          2        1         0
  AMP PEAK 20(13Q33.3) WILD-TYPE          6          5        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 20(13Q33.3) MUTATED           0
  AMP PEAK 20(13Q33.3) WILD-TYPE         2
D20V3, multiclass
            clus
vv           AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  STAGE I                              29                            117
  STAGE II                             14                             58
  STAGE III                             0                              2
  STAGE IIIA                           11                             41
  STAGE IIIB                            1                              6
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(13Q33.3) MUTATED      31  15  12   2
  AMP PEAK 20(13Q33.3) WILD-TYPE   124  63  52  10
D20V4, multiclass
       clus
vv      AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  T0+T1                           31                            124
  T2                              15                             63
  T3                              12                             52
  T4                               2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED    43   1
  AMP PEAK 20(13Q33.3) WILD-TYPE 179   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     43    1
  AMP PEAK 20(13Q33.3) WILD-TYPE  179    2
   clus
vv  AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  0                           43                            179
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 20(13Q33.3) MUTATED    48   1  11
  AMP PEAK 20(13Q33.3) WILD-TYPE 190   3  58
D20V6, multiclass
    clus
vv   AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  M0                           48                            190
  M1                            1                              3
  MX                           11                             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED    23  37
  AMP PEAK 20(13Q33.3) WILD-TYPE  77 174
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED     23   37
  AMP PEAK 20(13Q33.3) WILD-TYPE   77  174
        clus
vv       AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  FEMALE                           23                             77
  MALE                             37                            174
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                         0
  AMP PEAK 20(13Q33.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 20(13Q33.3) MUTATED                         57
  AMP PEAK 20(13Q33.3) WILD-TYPE                      246
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 20(13Q33.3) MUTATED                                  3
  AMP PEAK 20(13Q33.3) WILD-TYPE                                3
D20V8, multiclass
                                  clus
vv                                 AMP PEAK 20(13Q33.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   57
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 AMP PEAK 20(13Q33.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    246
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              3
[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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(13Q33.3) MUTATED    51   3   0   4
  AMP PEAK 20(13Q33.3) WILD-TYPE 223  11   1  12
D20V9, multiclass
    clus
vv   AMP PEAK 20(13Q33.3) MUTATED AMP PEAK 20(13Q33.3) WILD-TYPE
  R0                           51                            223
  R1                            3                             11
  R2                            0                              1
  RX                            4                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(13Q33.3) MUTATED                                  0    32
  AMP PEAK 20(13Q33.3) WILD-TYPE                                1   109
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(13Q33.3) MUTATED                           5    21
  AMP PEAK 20(13Q33.3) WILD-TYPE                        10   124
D20V10, multiclass
                                  clus
vv                                 AMP PEAK 20(13Q33.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      32
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      21
                                  clus
vv                                 AMP PEAK 20(13Q33.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       109
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       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"
D20V11, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q33.3) MUTATED     2  53
  AMP PEAK 20(13Q33.3) WILD-TYPE   6 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q33.3) MUTATED      2   53
  AMP PEAK 20(13Q33.3) WILD-TYPE    6  234
                        clus
vv                       AMP PEAK 20(13Q33.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       AMP PEAK 20(13Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            234
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(15Q26.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(15Q26.3) MUTATED    33  10
  AMP PEAK 21(15Q26.3) WILD-TYPE 167  82
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            43                            249 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            10                             82 
$`AMP PEAK 21(15Q26.3) MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BW-A5NO 
       10.78        37.32        23.34        13.84         0.26         0.66 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A11A TCGA-DD-A39Z TCGA-DD-A4NI 
        3.39         4.24         0.10         2.60        19.76        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AACZ 
       30.51        78.84       100.96        59.18        13.15         5.62 
TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 
        3.02         8.28         9.86         9.86         4.64        11.31 
TCGA-DD-AAEA TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A2KA 
       14.79        15.85        13.35         0.20         0.20        11.74 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A3CH 
       22.85        32.45         0.39        51.06        14.86        25.64 
TCGA-G3-A6UC TCGA-MI-A75G TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7SK TCGA-UB-A7MA 
        7.76        18.38        10.85         4.44        15.52        14.96 
TCGA-WQ-AB4B 
        4.01 

$`AMP PEAK 21(15Q26.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       46.78        27.52        27.52         2.99        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       69.57         5.03        44.42        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
       12.72         7.46        13.45         4.80         0.07         2.86 
TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        0.39         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       73.38        30.97        30.15        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       73.81       108.76        12.26         0.30        80.75        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
        9.30         7.56        10.98         1.45        27.72        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        65.75        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59         4.50        18.54        21.63        33.83        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        31.53        30.58        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
        3.78        25.08        24.00        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADW 
       17.33         3.95         5.29        57.27         7.10         6.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
        9.67         9.63         9.47         8.52        12.56        12.69 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       12.16        15.45        16.37        15.65        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        79.10        72.26        59.93        61.87        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       13.41        12.69        13.91         0.23         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        13.15        13.41         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        60.36         1.22        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        58.49        21.53        22.13         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 
       19.23        14.70        11.97        20.42        17.10        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.84        13.38        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
        9.57        16.67        12.85        20.71        58.88        16.37 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
       21.01         2.04        21.04        19.04        15.39        24.13 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         1.02         0.99        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                        100.96                         113.00 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                         11.74                          15.42 
[1] "0.1 - 101.0 (11.7)" "0.0 - 113.0 (15.4)"
[1] "hr=" "1.1"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 21(15Q26.3) MUTATED        17       12         0         11
  AMP PEAK 21(15Q26.3) WILD-TYPE     129       60         2         41
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(15Q26.3) MUTATED            2          1        1         0
  AMP PEAK 21(15Q26.3) WILD-TYPE          5          6        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 21(15Q26.3) MUTATED           0
  AMP PEAK 21(15Q26.3) WILD-TYPE         2
D21V3, multiclass
            clus
vv           AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  STAGE I                              17                            129
  STAGE II                             12                             60
  STAGE III                             0                              2
  STAGE IIIA                           11                             41
  STAGE IIIB                            2                              5
  STAGE IIIC                            1                              6
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(15Q26.3) MUTATED      17  14  12   3
  AMP PEAK 21(15Q26.3) WILD-TYPE   138  64  52   9
D21V4, multiclass
       clus
vv      AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  T0+T1                           17                            138
  T2                              14                             64
  T3                              12                             52
  T4                               3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED    33   0
  AMP PEAK 21(15Q26.3) WILD-TYPE 189   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     33    0
  AMP PEAK 21(15Q26.3) WILD-TYPE  189    3
   clus
vv  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  0                           33                            189
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 21(15Q26.3) MUTATED    38   1   7
  AMP PEAK 21(15Q26.3) WILD-TYPE 200   3  62
D21V6, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  M0                           38                            200
  M1                            1                              3
  MX                            7                             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED    18  28
  AMP PEAK 21(15Q26.3) WILD-TYPE  82 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     18   28
  AMP PEAK 21(15Q26.3) WILD-TYPE   82  183
        clus
vv       AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  FEMALE                           18                             82
  MALE                             28                            183
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 21(15Q26.3) MUTATED                         1
  AMP PEAK 21(15Q26.3) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 21(15Q26.3) MUTATED                         44
  AMP PEAK 21(15Q26.3) WILD-TYPE                      259
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 21(15Q26.3) MUTATED                                  1
  AMP PEAK 21(15Q26.3) WILD-TYPE                                5
D21V8, multiclass
                                  clus
vv                                 AMP PEAK 21(15Q26.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   44
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 AMP PEAK 21(15Q26.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    259
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              5
[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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(15Q26.3) MUTATED    38   3   0   4
  AMP PEAK 21(15Q26.3) WILD-TYPE 236  11   1  12
D21V9, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  R0                           38                            236
  R1                            3                             11
  R2                            0                              1
  RX                            4                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(15Q26.3) MUTATED                                  0    22
  AMP PEAK 21(15Q26.3) WILD-TYPE                                1   119
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(15Q26.3) MUTATED                           2    20
  AMP PEAK 21(15Q26.3) WILD-TYPE                        13   125
D21V10, multiclass
                                  clus
vv                                 AMP PEAK 21(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      22
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      20
                                  clus
vv                                 AMP PEAK 21(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       119
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED     2  40
  AMP PEAK 21(15Q26.3) WILD-TYPE   6 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      2   40
  AMP PEAK 21(15Q26.3) WILD-TYPE    6  247
                        clus
vv                       AMP PEAK 21(15Q26.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       AMP PEAK 21(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            247
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(17P11.2) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(17P11.2) MUTATED    23  13
  AMP PEAK 22(17P11.2) WILD-TYPE 177  79
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            36                            256 
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                            13                             79 
$`AMP PEAK 22(17P11.2) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5260 TCGA-CC-A3M9 
       27.91        37.32        13.84         0.26         2.86         0.10 
TCGA-DD-A115 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 
       83.57         7.33         2.60        17.59       102.74        13.78 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73E TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AAD0 
       73.81       108.76         1.45        59.18        53.19         4.50 
TCGA-DD-AADD TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AAVR TCGA-ED-A66X TCGA-ED-A66Y 
       28.41         3.02        57.27        72.26        13.35         0.23 
TCGA-ED-A7PZ TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZP 
        0.20         0.20        11.74        10.98        22.85        60.36 
TCGA-G3-AAUZ TCGA-G3-AAV6 TCGA-MI-A75G TCGA-O8-A75V TCGA-UB-A7MA TCGA-UB-A7MB 
       11.24         2.14        18.38         4.44        14.96        17.29 

$`AMP PEAK 22(17P11.2) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-A10R 
        7.10        10.78        10.59         0.66        48.99        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        69.57         5.03        44.42        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       14.60        12.72         7.46        13.45         4.80         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        0.07         0.39         3.39         4.24         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        79.73        37.78        53.33       113.00 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 
        5.62        19.76        25.81         7.66        70.06        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       29.56        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        9.30         7.56        10.98        27.72       100.96        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        65.75        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       58.16        13.15        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59         5.62        18.54        21.63        33.83        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF 
       22.09        31.53        30.58        29.26        13.97         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       25.08        24.00        24.13        20.91         0.39        17.33 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        3.95         5.29         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.86         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.91         0.20         0.20         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20         0.20        18.74        19.99         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        32.45        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       12.03         5.98         1.84         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.17         0.89         3.02         1.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       16.67        12.85        20.71        10.85        58.88        16.37 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       21.01         2.04        21.04        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       24.13        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
        4.57         1.02         0.99         4.01        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                        108.76                         113.00 
  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE 
                         13.81                          14.65 
[1] "0.1 - 108.8 (13.8)" "0.0 - 113.0 (14.6)"
[1] "hr=" "1"  
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 22(17P11.2) MUTATED        16        6         1         12
  AMP PEAK 22(17P11.2) WILD-TYPE     130       66         1         40
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(17P11.2) MUTATED            2          1        1         0
  AMP PEAK 22(17P11.2) WILD-TYPE          5          6        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 22(17P11.2) MUTATED           0
  AMP PEAK 22(17P11.2) WILD-TYPE         2
D22V3, multiclass
            clus
vv           AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  STAGE I                              16                            130
  STAGE II                              6                             66
  STAGE III                             1                              1
  STAGE IIIA                           12                             40
  STAGE IIIB                            2                              5
  STAGE IIIC                            1                              6
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(17P11.2) MUTATED      16   7  15   2
  AMP PEAK 22(17P11.2) WILD-TYPE   139  71  49  10
D22V4, multiclass
       clus
vv      AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  T0+T1                           16                            139
  T2                               7                             71
  T3                              15                             49
  T4                               2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                                cls
clus                               0   1
  AMP PEAK 22(17P11.2) MUTATED    30   0
  AMP PEAK 22(17P11.2) WILD-TYPE 192   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED     30    0
  AMP PEAK 22(17P11.2) WILD-TYPE  192    3
   clus
vv  AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  0                           30                            192
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 22(17P11.2) MUTATED    32   1   7
  AMP PEAK 22(17P11.2) WILD-TYPE 206   3  62
D22V6, multiclass
    clus
vv   AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  M0                           32                            206
  M1                            1                              3
  MX                            7                             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(17P11.2) MUTATED    13  27
  AMP PEAK 22(17P11.2) WILD-TYPE  87 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED     13   27
  AMP PEAK 22(17P11.2) WILD-TYPE   87  184
        clus
vv       AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  FEMALE                           13                             87
  MALE                             27                            184
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 22(17P11.2) MUTATED                         0
  AMP PEAK 22(17P11.2) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 22(17P11.2) MUTATED                         39
  AMP PEAK 22(17P11.2) WILD-TYPE                      264
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 22(17P11.2) MUTATED                                  1
  AMP PEAK 22(17P11.2) WILD-TYPE                                5
D22V8, multiclass
                                  clus
vv                                 AMP PEAK 22(17P11.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   39
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 AMP PEAK 22(17P11.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    264
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              5
[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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(17P11.2) MUTATED    32   5   1   2
  AMP PEAK 22(17P11.2) WILD-TYPE 242   9   0  14
D22V9, multiclass
    clus
vv   AMP PEAK 22(17P11.2) MUTATED AMP PEAK 22(17P11.2) WILD-TYPE
  R0                           32                            242
  R1                            5                              9
  R2                            1                              0
  RX                            2                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(17P11.2) MUTATED                                  0    19
  AMP PEAK 22(17P11.2) WILD-TYPE                                1   122
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(17P11.2) MUTATED                           1    17
  AMP PEAK 22(17P11.2) WILD-TYPE                        14   128
D22V10, multiclass
                                  clus
vv                                 AMP PEAK 22(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      19
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      17
                                  clus
vv                                 AMP PEAK 22(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       122
  BLACK OR AFRICAN AMERICAN                                    14
  WHITE                                                       128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                                cls
clus                               0   1
  AMP PEAK 22(17P11.2) MUTATED     2  34
  AMP PEAK 22(17P11.2) WILD-TYPE   6 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17P11.2) MUTATED      2   34
  AMP PEAK 22(17P11.2) WILD-TYPE    6  253
                        clus
vv                       AMP PEAK 22(17P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           34
                        clus
vv                       AMP PEAK 22(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(17Q25.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(17Q25.3) MUTATED    76  38
  AMP PEAK 23(17Q25.3) WILD-TYPE 124  54
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           114                            178 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                            38                             54 
$`AMP PEAK 23(17Q25.3) MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y 
       48.99        37.32        27.52        27.52         2.99        23.34 
TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
        1.12         5.03        44.42        13.84        22.36        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB 
       13.45         0.66         2.86         0.39         4.24         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y 
       21.76        79.40        66.31         6.02        29.16         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A7 TCGA-DD-A3A9 
       25.81         7.66        17.59        20.12        13.78        30.61 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73A 
       30.15        26.83        30.51        73.81       108.76        10.98 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       10.98         1.45        27.72         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACS TCGA-DD-AACX 
       59.18        63.48        53.19        60.10        48.49         5.59 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN 
       34.09        22.09        13.97        28.41         3.78        17.33 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE2 
        3.02        57.27         8.28         6.67         9.86         9.47 
TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVR TCGA-ED-A66X 
        9.86        14.79        16.37        35.08        72.26        13.35 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC 
        0.23         0.20        13.15         0.20        10.98         0.62 
TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
       22.85        19.10         0.03         0.33        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A3CK 
       53.79        30.74        58.49        21.53        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV1 
       14.70        11.97        20.42        12.03        11.24        11.80 
TCGA-G3-AAV6 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I 
        2.14        24.36        12.72         5.92        18.38        20.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MA 
       58.88        16.37         4.44        21.01        24.13        14.96 
TCGA-UB-A7MC TCGA-UB-AA0U TCGA-ZP-A9CZ TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       14.40         8.32        23.21        24.43        12.99        74.24 

$`AMP PEAK 23(17Q25.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.78        10.59         0.66        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I 
       46.78        25.32        69.57         0.26         9.50        12.72 
TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        7.46         4.80         0.07         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
        0.07        79.73       113.00         0.46        51.29        90.71 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A2 
       18.35        13.64        21.14        55.69        19.76        70.06 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      102.74       107.11         0.36        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.97        39.78        56.25        29.56        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73G TCGA-DD-AA3A 
       80.75        78.84         9.30         7.56       100.96        13.48 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK 
       55.40        12.53        12.00        15.42         6.41         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        13.15        14.33        40.77        38.04 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 
        5.62         4.50        18.54        21.63        33.83        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       30.58        29.26        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADY TCGA-DD-AAE1 
        0.39         3.95         5.29         7.10         9.67         9.63 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
        8.52         4.64        12.56        11.31        12.69        12.16 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS 
       15.45        15.65        15.65        79.07        79.10        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       61.87        61.38        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        47.70        13.41        12.69        15.85        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20         0.20         0.20        13.41         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        11.74         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        23.97        27.88         8.12         6.38         0.13 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
        0.39        51.06        28.27        14.86        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 
        5.92        17.10         7.76         5.98         1.84         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         9.17         0.89         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       11.84        13.38         4.27         9.57        16.67        12.85 
TCGA-MR-A8JO TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       10.85         2.04        21.04        19.04        15.39        15.52 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       17.29         1.71        15.98         7.04         4.57         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
        0.99         4.01        13.55         4.67        25.71        23.57 
TCGA-ZP-A9D1 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
        0.69        45.57        35.05         8.22 

  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                        108.76                         113.00 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                        16.370                         13.515 
[1] "0.0 - 108.8 (16.4)" "0.1 - 113.0 (13.5)"
[1] "hr=" "1.1"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 23(17Q25.3) MUTATED        50       29         0         28
  AMP PEAK 23(17Q25.3) WILD-TYPE      96       43         2         24
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(17Q25.3) MUTATED            5          3        1         0
  AMP PEAK 23(17Q25.3) WILD-TYPE          2          4        1         1
                                vv
clus                             STAGE IVB
  AMP PEAK 23(17Q25.3) MUTATED           1
  AMP PEAK 23(17Q25.3) WILD-TYPE         1
D23V3, multiclass
            clus
vv           AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  STAGE I                              50                             96
  STAGE II                             29                             43
  STAGE III                             0                              2
  STAGE IIIA                           28                             24
  STAGE IIIB                            5                              2
  STAGE IIIC                            3                              4
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 23(17Q25.3) MUTATED      53  33  33   8
  AMP PEAK 23(17Q25.3) WILD-TYPE   102  45  31   4
D23V4, multiclass
       clus
vv      AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  T0+T1                           53                            102
  T2                              33                             45
  T3                              33                             31
  T4                               8                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED    88   1
  AMP PEAK 23(17Q25.3) WILD-TYPE 134   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED     88    1
  AMP PEAK 23(17Q25.3) WILD-TYPE  134    2
   clus
vv  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  0                           88                            134
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 23(17Q25.3) MUTATED   100   2  25
  AMP PEAK 23(17Q25.3) WILD-TYPE 138   2  44
D23V6, multiclass
    clus
vv   AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  M0                          100                            138
  M1                            2                              2
  MX                           25                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED    34  93
  AMP PEAK 23(17Q25.3) WILD-TYPE  66 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED     34   93
  AMP PEAK 23(17Q25.3) WILD-TYPE   66  118
        clus
vv       AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  FEMALE                           34                             66
  MALE                             93                            118
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  AMP PEAK 23(17Q25.3) MUTATED                         0
  AMP PEAK 23(17Q25.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  AMP PEAK 23(17Q25.3) MUTATED                        126
  AMP PEAK 23(17Q25.3) WILD-TYPE                      177
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 23(17Q25.3) MUTATED                                  1
  AMP PEAK 23(17Q25.3) WILD-TYPE                                5
D23V8, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q25.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  126
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 AMP PEAK 23(17Q25.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    177
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              5
[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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(17Q25.3) MUTATED   107  10   1   8
  AMP PEAK 23(17Q25.3) WILD-TYPE 167   4   0   8
D23V9, multiclass
    clus
vv   AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  R0                          107                            167
  R1                           10                              4
  R2                            1                              0
  RX                            8                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(17Q25.3) MUTATED                                  1    62
  AMP PEAK 23(17Q25.3) WILD-TYPE                                0    79
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(17Q25.3) MUTATED                           7    51
  AMP PEAK 23(17Q25.3) WILD-TYPE                         8    94
D23V10, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      62
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      51
                                  clus
vv                                 AMP PEAK 23(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        79
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                        94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED     3 117
  AMP PEAK 23(17Q25.3) WILD-TYPE   5 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED      3  117
  AMP PEAK 23(17Q25.3) WILD-TYPE    5  170
                        clus
vv                       AMP PEAK 23(17Q25.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          117
                        clus
vv                       AMP PEAK 23(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            170
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(19P13.12) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 24(19P13.12) MUTATED    35  21
  AMP PEAK 24(19P13.12) WILD-TYPE 165  71
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             56                             236 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                             21                              71 
$`AMP PEAK 24(19P13.12) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A112 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 
       37.32        10.13         5.03        13.45         0.66         0.39 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF 
       79.73       113.00         7.33        90.71        19.79        12.95 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN 
       21.14        55.69        13.78        30.61        73.38        29.56 
TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACL TCGA-DD-AAD5 TCGA-DD-AADA 
       73.81        78.84       100.96         1.91        34.09        30.58 
TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 
       29.26         3.78         9.86         9.86         4.64        12.69 
TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVR TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E 
       15.65        35.08        72.26        13.35         0.23        13.41 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A3I0 
       11.74        10.98         0.62        22.85        23.97        27.88 
TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M7 
        8.12        60.36        51.06        58.49        17.10         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 TCGA-KR-A7K2 TCGA-RC-A7S9 TCGA-UB-A7MA 
       11.24         8.55         3.02        11.84        21.04        14.96 
TCGA-YA-A8S7 TCGA-ZP-A9D1 
       13.55         0.69 

$`AMP PEAK 24(19P13.12) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 
        9.50        14.60        12.72         7.46         4.80         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A 
        0.10         0.13        37.78        83.57        53.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        21.76        51.29        79.40        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
        6.71        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       56.25       108.76        12.26         0.30        80.75        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
        9.30         7.56        10.98         1.45        27.72        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        65.75        59.18        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       63.48        12.00        15.42         6.41        53.19        60.10 
TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        0.30        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI 
       33.83        22.09        31.53        13.97        28.41        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       24.00        24.13        20.91         0.39        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.95         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.67         9.63         9.47         8.52        12.56        11.31 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP 
       14.79        12.16        15.45        16.37        15.65        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       79.10        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       15.85        13.91         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3R2 
        9.96        11.93        14.40        32.45        19.10         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.13         0.03         0.33         0.39         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        7.76        12.03         1.84        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         2.14         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72         5.92         4.27         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85        20.71        10.85        58.88        16.37         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.01         2.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         1.02         0.99         4.01         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.21        23.57        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                           0.23                            0.03 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                         113.00                          108.76 
  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE 
                          14.37                           14.50 
[1] "0.2 - 113.0 (14.4)" "0.0 - 108.8 (14.5)"
[1] "hr=" "1"  
D24V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 24(19P13.12) MUTATED        27       11         0         11
  AMP PEAK 24(19P13.12) WILD-TYPE     119       61         2         41
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 24(19P13.12) MUTATED            1          0        2         1
  AMP PEAK 24(19P13.12) WILD-TYPE          6          7        0         0
                                 vv
clus                              STAGE IVB
  AMP PEAK 24(19P13.12) MUTATED           1
  AMP PEAK 24(19P13.12) WILD-TYPE         1
D24V3, multiclass
            clus
vv           AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  STAGE I                               27                             119
  STAGE II                              11                              61
  STAGE III                              0                               2
  STAGE IIIA                            11                              41
  STAGE IIIB                             1                               6
  STAGE IIIC                             0                               7
  STAGE IV                               2                               0
  STAGE IVA                              1                               0
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 24(19P13.12) MUTATED      29  13  15   1
  AMP PEAK 24(19P13.12) WILD-TYPE   126  65  49  11
D24V4, multiclass
       clus
vv      AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  T0+T1                            29                             126
  T2                               13                              65
  T3                               15                              49
  T4                                1                              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED    42   1
  AMP PEAK 24(19P13.12) WILD-TYPE 180   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED     42    1
  AMP PEAK 24(19P13.12) WILD-TYPE  180    2
   clus
vv  AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  0                            42                             180
  1                             1                               2
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  AMP PEAK 24(19P13.12) MUTATED    42   3  13
  AMP PEAK 24(19P13.12) WILD-TYPE 196   1  56
D24V6, multiclass
    clus
vv   AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  M0                            42                             196
  M1                             3                               1
  MX                            13                              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED    29  29
  AMP PEAK 24(19P13.12) WILD-TYPE  71 182
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED     29   29
  AMP PEAK 24(19P13.12) WILD-TYPE   71  182
        clus
vv       AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  FEMALE                            29                              71
  MALE                              29                             182
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 24(19P13.12) MUTATED                         0
  AMP PEAK 24(19P13.12) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 24(19P13.12) MUTATED                         55
  AMP PEAK 24(19P13.12) WILD-TYPE                      248
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 24(19P13.12) MUTATED                                  3
  AMP PEAK 24(19P13.12) WILD-TYPE                                3
D24V8, multiclass
                                  clus
vv                                 AMP PEAK 24(19P13.12) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    55
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
                                  clus
vv                                 AMP PEAK 24(19P13.12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     248
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               3
[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"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 24(19P13.12) MUTATED    51   3   1   3
  AMP PEAK 24(19P13.12) WILD-TYPE 223  11   0  13
D24V9, multiclass
    clus
vv   AMP PEAK 24(19P13.12) MUTATED AMP PEAK 24(19P13.12) WILD-TYPE
  R0                            51                             223
  R1                             3                              11
  R2                             1                               0
  RX                             3                              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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(19P13.12) MUTATED                                  0    22
  AMP PEAK 24(19P13.12) WILD-TYPE                                1   119
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(19P13.12) MUTATED                           3    31
  AMP PEAK 24(19P13.12) WILD-TYPE                        12   114
D24V10, multiclass
                                  clus
vv                                 AMP PEAK 24(19P13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       22
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                       31
                                  clus
vv                                 AMP PEAK 24(19P13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        119
  BLACK OR AFRICAN AMERICAN                                     12
  WHITE                                                        114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                                 cls
clus                                0   1
  AMP PEAK 24(19P13.12) MUTATED     3  53
  AMP PEAK 24(19P13.12) WILD-TYPE   5 234
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(19P13.12) MUTATED      3   53
  AMP PEAK 24(19P13.12) WILD-TYPE    5  234
                        clus
vv                       AMP PEAK 24(19P13.12) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       AMP PEAK 24(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             234
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(19Q12) MUTATION ANALYSIS
D25V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 25(19Q12) MUTATED    40  23
  AMP PEAK 25(19Q12) WILD-TYPE 160  69
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          63                          229 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          23                           69 
$`AMP PEAK 25(19Q12) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BD-A3EP TCGA-BW-A5NO 
       37.32        10.13        27.52         5.03        13.45         0.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 
        2.86         0.39        79.73       113.00         7.33        90.71 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A39V TCGA-DD-A3A7 
       19.79        12.95        45.11         6.02        21.14        13.78 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV 
       30.61        73.38        29.56        73.81        12.26        78.84 
TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACP TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADM 
      100.96        15.42        13.15        29.26         3.78         0.39 
TCGA-DD-AAE0 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEK TCGA-DD-AAVW TCGA-ED-A66X 
        9.86         8.52        12.56        35.08        61.38        13.35 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC 
        0.23         0.20         0.20        13.41        10.98         0.62 
TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X 
       22.85        23.97        27.88         0.39        51.06        58.49 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-KR-A7K2 TCGA-MI-A75G 
       17.10        12.03         5.98         8.55        11.84        18.38 
TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7ME TCGA-WJ-A86L 
       16.37        21.04        15.39        14.96        15.98         1.02 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
        4.01        13.55         0.69 

$`AMP PEAK 25(19Q12) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57        44.42        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5262 
       14.60        12.72         7.46         4.80         0.07         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       37.78        83.57        53.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       51.29        79.40        66.31        75.65         6.71        49.15 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       29.16        18.35        13.64        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11         0.36        33.14        32.52        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR 
       26.83        30.51        39.78        56.25       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       27.72        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        63.48        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS 
       60.10         0.30         1.91        58.16        14.33        48.49 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       40.77        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       13.97        28.41        25.08        24.00        24.13        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       17.33         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
        8.28         6.67         9.67         9.63         9.47         9.86 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        15.65        15.65        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        61.87        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        47.70        13.41        12.69        15.85        13.91 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        11.74         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36         1.22        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M9 
       19.23        14.70        11.97        20.42         7.76         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
       11.24        11.80         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06         4.01         2.14        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
        5.92         4.27         9.57        16.67        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF 
       10.85        58.88         4.44        21.01         2.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
       15.52        24.13        17.29        14.40         1.71         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        8.32         4.57         0.99         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                        0.20                         0.03 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                      113.00                       108.76 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                       13.55                        14.70 
[1] "0.2 - 113.0 (13.6)" "0.0 - 108.8 (14.7)"
[1] "hr=" "1.2"
D25V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(19Q12) MUTATED        28       16         0         10          1
  AMP PEAK 25(19Q12) WILD-TYPE     118       56         2         42          6
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 25(19Q12) MUTATED            1        2         1         1
  AMP PEAK 25(19Q12) WILD-TYPE          6        0         0         1
D25V3, multiclass
            clus
vv           AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  STAGE I                            28                          118
  STAGE II                           16                           56
  STAGE III                           0                            2
  STAGE IIIA                         10                           42
  STAGE IIIB                          1                            6
  STAGE IIIC                          1                            6
  STAGE IV                            2                            0
  STAGE IVA                           1                            0
  STAGE IVB                           1                            1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  AMP PEAK 25(19Q12) MUTATED      30  18  14   3
  AMP PEAK 25(19Q12) WILD-TYPE   125  60  50   9
D25V4, multiclass
       clus
vv      AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  T0+T1                         30                          125
  T2                            18                           60
  T3                            14                           50
  T4                             3                            9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    44   1
  AMP PEAK 25(19Q12) WILD-TYPE 178   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     44    1
  AMP PEAK 25(19Q12) WILD-TYPE  178    2
   clus
vv  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  0                         44                          178
  1                          1                            2
[1] 2 2
[1] FALSE
                              vv
clus                            M0  M1  MX
  AMP PEAK 25(19Q12) MUTATED    46   3  16
  AMP PEAK 25(19Q12) WILD-TYPE 192   1  53
D25V6, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  M0                         46                          192
  M1                          3                            1
  MX                         16                           53
[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"
D25V7, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    26  39
  AMP PEAK 25(19Q12) WILD-TYPE  74 172
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     26   39
  AMP PEAK 25(19Q12) WILD-TYPE   74  172
        clus
vv       AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  FEMALE                         26                           74
  MALE                           39                          172
[1] 2 2
[1] FALSE
                              vv
clus                           FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                         0                       62
  AMP PEAK 25(19Q12) WILD-TYPE                       2                      241
                              vv
clus                           HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 25(19Q12) MUTATED                                  3
  AMP PEAK 25(19Q12) WILD-TYPE                                3
D25V8, multiclass
                                  clus
vv                                 AMP PEAK 25(19Q12) MUTATED
  FIBROLAMELLAR CARCINOMA                                   0
  HEPATOCELLULAR CARCINOMA                                 62
  HEPATOCHOLANGIOCARCINOMA (MIXED)                          3
                                  clus
vv                                 AMP PEAK 25(19Q12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                  241
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
[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"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 25(19Q12) MUTATED    57   3   1   4
  AMP PEAK 25(19Q12) WILD-TYPE 217  11   0  12
D25V9, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  R0                         57                          217
  R1                          3                           11
  R2                          1                            0
  RX                          4                           12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(19Q12) MUTATED                                  0    25
  AMP PEAK 25(19Q12) WILD-TYPE                                1   116
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(19Q12) MUTATED                           3    36
  AMP PEAK 25(19Q12) WILD-TYPE                        12   109
D25V10, multiclass
                                  clus
vv                                 AMP PEAK 25(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                    25
  BLACK OR AFRICAN AMERICAN                                 3
  WHITE                                                    36
                                  clus
vv                                 AMP PEAK 25(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                     116
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED     3  60
  AMP PEAK 25(19Q12) WILD-TYPE   5 227
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED      3   60
  AMP PEAK 25(19Q12) WILD-TYPE    5  227
                        clus
vv                       AMP PEAK 25(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         60
                        clus
vv                       AMP PEAK 25(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          227
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(19Q13.11) MUTATION ANALYSIS
D26V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 26(19Q13.11) MUTATED    45  29
  AMP PEAK 26(19Q13.11) WILD-TYPE 155  63
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             74                             218 
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                             29                              63 
$`AMP PEAK 26(19Q13.11) MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 
       37.32        10.13        27.52        23.34         5.03        13.84 
TCGA-BC-A3KG TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-DD-A113 
       22.36        13.45         0.66         0.39         0.10        79.73 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG 
      113.00         7.33        90.71        19.79        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND 
        6.02        13.64        21.14        13.78        30.61        73.38 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73F TCGA-DD-A73G 
       29.56        73.81        12.26        78.84        27.72       100.96 
TCGA-DD-AACG TCGA-DD-AACP TCGA-DD-AACW TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       15.42        13.15        38.04        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEK 
        3.78         0.39         9.86        12.56        14.79        35.08 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KA 
       13.35         0.23         0.20         0.20        13.41        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A495 
       10.98         0.62        22.85        23.97        27.88         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 
        0.39        51.06        58.49        17.10        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-GJ-A6C0 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A8LF 
        1.84         8.55         1.02        11.84        18.38        16.37 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7ME TCGA-WQ-AB4B TCGA-YA-A8S7 
       21.01        21.04        15.39        15.98         4.01        13.55 
TCGA-ZP-A9D1 TCGA-ZS-A9CF 
        0.69        74.24 

$`AMP PEAK 26(19Q13.11) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 
       46.78        27.52         2.99        25.32         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       44.42         0.26         9.50        14.60        12.72         7.46 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.80         0.07         2.86         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10         0.13        37.78        83.57        53.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        21.76        51.29        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X 
       75.65         6.71        49.15        29.16        18.35        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
      108.76         0.30        80.75        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       10.98         1.45        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       59.18        55.40        12.53        63.48        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
       53.19        60.10         0.30         1.91        58.16        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        40.77         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO 
       25.08        24.00        24.13        20.91        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.95         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.67         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       11.31        12.69        12.16        15.45        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       15.65        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       47.70        13.41        12.69        15.85        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        13.15         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
       19.99         9.96        11.93        14.40        32.45        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        8.12         6.38         0.13         0.33        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       20.42         7.76        11.24        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         2.14         3.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SF 
       20.71        10.85        58.88         4.44         2.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-ZP-A9CV 
        7.04         8.32         4.57         1.02         0.99         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       35.05         8.22 

  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                           0.03                            0.07 
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                         113.00                          108.76 
  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE 
                         13.905                          14.650 
[1] "0.0 - 113.0 (13.9)" "0.1 - 108.8 (14.6)"
[1] "hr=" "1.3"
D26V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 26(19Q13.11) MUTATED        31       21         0         14
  AMP PEAK 26(19Q13.11) WILD-TYPE     115       51         2         38
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 26(19Q13.11) MUTATED            3          0        2         1
  AMP PEAK 26(19Q13.11) WILD-TYPE          4          7        0         0
                                 vv
clus                              STAGE IVB
  AMP PEAK 26(19Q13.11) MUTATED           1
  AMP PEAK 26(19Q13.11) WILD-TYPE         1
D26V3, multiclass
            clus
vv           AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  STAGE I                               31                             115
  STAGE II                              21                              51
  STAGE III                              0                               2
  STAGE IIIA                            14                              38
  STAGE IIIB                             3                               4
  STAGE IIIC                             0                               7
  STAGE IV                               2                               0
  STAGE IVA                              1                               0
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 26(19Q13.11) MUTATED      33  23  19   4
  AMP PEAK 26(19Q13.11) WILD-TYPE   122  55  45   8
D26V4, multiclass
       clus
vv      AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  T0+T1                            33                             122
  T2                               23                              55
  T3                               19                              45
  T4                                4                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED    51   1
  AMP PEAK 26(19Q13.11) WILD-TYPE 171   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED     51    1
  AMP PEAK 26(19Q13.11) WILD-TYPE  171    2
   clus
vv  AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  0                            51                             171
  1                             1                               2
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  AMP PEAK 26(19Q13.11) MUTATED    55   3  21
  AMP PEAK 26(19Q13.11) WILD-TYPE 183   1  48
D26V6, multiclass
    clus
vv   AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  M0                            55                             183
  M1                             3                               1
  MX                            21                              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED    31  48
  AMP PEAK 26(19Q13.11) WILD-TYPE  69 163
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED     31   48
  AMP PEAK 26(19Q13.11) WILD-TYPE   69  163
        clus
vv       AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  FEMALE                            31                              69
  MALE                              48                             163
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 26(19Q13.11) MUTATED                         0
  AMP PEAK 26(19Q13.11) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 26(19Q13.11) MUTATED                         77
  AMP PEAK 26(19Q13.11) WILD-TYPE                      226
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 26(19Q13.11) MUTATED                                  2
  AMP PEAK 26(19Q13.11) WILD-TYPE                                4
D26V8, multiclass
                                  clus
vv                                 AMP PEAK 26(19Q13.11) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    77
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 26(19Q13.11) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     226
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               4
[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"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 26(19Q13.11) MUTATED    70   2   1   5
  AMP PEAK 26(19Q13.11) WILD-TYPE 204  12   0  11
D26V9, multiclass
    clus
vv   AMP PEAK 26(19Q13.11) MUTATED AMP PEAK 26(19Q13.11) WILD-TYPE
  R0                            70                             204
  R1                             2                              12
  R2                             1                               0
  RX                             5                              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(19Q13.11) MUTATED                                  0    29
  AMP PEAK 26(19Q13.11) WILD-TYPE                                1   112
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(19Q13.11) MUTATED                           4    45
  AMP PEAK 26(19Q13.11) WILD-TYPE                        11   100
D26V10, multiclass
                                  clus
vv                                 AMP PEAK 26(19Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       29
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       45
                                  clus
vv                                 AMP PEAK 26(19Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        112
  BLACK OR AFRICAN AMERICAN                                     11
  WHITE                                                        100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                                 cls
clus                                0   1
  AMP PEAK 26(19Q13.11) MUTATED     3  73
  AMP PEAK 26(19Q13.11) WILD-TYPE   5 214
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(19Q13.11) MUTATED      3   73
  AMP PEAK 26(19Q13.11) WILD-TYPE    5  214
                        clus
vv                       AMP PEAK 26(19Q13.11) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            73
                        clus
vv                       AMP PEAK 26(19Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             214
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(20Q13.13) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 27(20Q13.13) MUTATED    61  35
  AMP PEAK 27(20Q13.13) WILD-TYPE 139  57
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                             96                             196 
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                             35                              57 
$`AMP PEAK 27(20Q13.13) MUTATED`
TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Y 
       10.59        48.99        37.32        10.13        27.52        23.34 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 
       13.84         0.26        14.60        13.45         0.66         0.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A118 TCGA-DD-A119 
        3.32         0.10         0.10         0.13       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
        2.60         0.46        21.76        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND 
       29.16        21.14       102.74        13.78        30.61        73.38 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 
       29.56        73.81         0.30        78.84       100.96         0.53 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACZ 
       59.18        55.40        53.19        13.15        48.49         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN 
        4.50        22.09        30.58        28.41         3.78        17.33 
TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 
        3.02         7.10         8.28         6.67         9.86         9.86 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
        4.64        12.69        14.79        15.65        15.65        35.08 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB 
       13.35         0.23         0.20        13.41         0.20        10.98 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3R2 TCGA-FV-A495 
        9.96        22.85        32.45        23.97         6.38         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 
        0.39         1.22        30.74        17.10        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.84        11.80         2.14         2.66        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       12.72        18.38        21.01        24.13        14.96        17.29 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZS-A9CD 
       15.98         8.32         0.99         4.01        13.55        45.57 

$`AMP PEAK 27(20Q13.13) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
        7.10        10.78         0.66        27.91        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        44.42 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 
       22.36         9.50        12.72         7.46         4.80         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 
        2.86         3.39         4.24         0.07        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       83.57        53.33        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65         6.71         6.02        18.35        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       17.59        20.12       107.11         0.36        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
      108.76        12.26        80.75        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
       10.98         1.45        27.72        13.48        11.41        65.75 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ 
       12.53        63.48        12.00        15.42         6.41        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW 
        0.30         1.91        58.16        14.33        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
        5.59        18.54        21.63        33.83        34.09        31.53 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       29.26        13.97        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE1 
        0.39         3.95         5.29        57.27         9.67         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEB TCGA-DD-AAED 
        9.47         8.52        12.56        11.31        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       16.37        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       47.70        13.41        12.69        15.85        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20         0.20        13.15         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       19.99        11.74         0.62        11.93        14.40        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T 
       27.88         8.12         0.13         0.33        60.36        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       20.42         7.76        11.24         8.55         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF 
        0.89         3.02         1.02         2.20        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06         4.01         2.14        24.36         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
       16.37         4.44         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       15.52        14.40         1.71         7.04         4.57         1.02 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        35.05        74.24         8.22 

  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                           0.03                            0.07 
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                         113.00                          108.76 
  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE 
                         13.365                          15.685 
[1] "0.0 - 113.0 (13.4)" "0.1 - 108.8 (15.7)"
[1] "hr=" "1.5"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 27(20Q13.13) MUTATED        44       20         2         23
  AMP PEAK 27(20Q13.13) WILD-TYPE     102       52         0         29
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 27(20Q13.13) MUTATED            5          2        1         1
  AMP PEAK 27(20Q13.13) WILD-TYPE          2          5        1         0
                                 vv
clus                              STAGE IVB
  AMP PEAK 27(20Q13.13) MUTATED           1
  AMP PEAK 27(20Q13.13) WILD-TYPE         1
D27V3, multiclass
            clus
vv           AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  STAGE I                               44                             102
  STAGE II                              20                              52
  STAGE III                              2                               0
  STAGE IIIA                            23                              29
  STAGE IIIB                             5                               2
  STAGE IIIC                             2                               5
  STAGE IV                               1                               1
  STAGE IVA                              1                               0
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 27(20Q13.13) MUTATED      46  21  31   6
  AMP PEAK 27(20Q13.13) WILD-TYPE   109  57  33   6
D27V4, multiclass
       clus
vv      AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  T0+T1                            46                             109
  T2                               21                              57
  T3                               31                              33
  T4                                6                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED    74   2
  AMP PEAK 27(20Q13.13) WILD-TYPE 148   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED     74    2
  AMP PEAK 27(20Q13.13) WILD-TYPE  148    1
   clus
vv  AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  0                            74                             148
  1                             2                               1
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  AMP PEAK 27(20Q13.13) MUTATED    83   2  19
  AMP PEAK 27(20Q13.13) WILD-TYPE 155   2  50
D27V6, multiclass
    clus
vv   AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  M0                            83                             155
  M1                             2                               2
  MX                            19                              50
[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"
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED    39  65
  AMP PEAK 27(20Q13.13) WILD-TYPE  61 146
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED     39   65
  AMP PEAK 27(20Q13.13) WILD-TYPE   61  146
        clus
vv       AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  FEMALE                            39                              61
  MALE                              65                             146
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 27(20Q13.13) MUTATED                         0
  AMP PEAK 27(20Q13.13) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 27(20Q13.13) MUTATED                        102
  AMP PEAK 27(20Q13.13) WILD-TYPE                      201
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 27(20Q13.13) MUTATED                                  2
  AMP PEAK 27(20Q13.13) WILD-TYPE                                4
D27V8, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.13) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                   102
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 27(20Q13.13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     201
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               4
[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"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 27(20Q13.13) MUTATED    89   6   1   5
  AMP PEAK 27(20Q13.13) WILD-TYPE 185   8   0  11
D27V9, multiclass
    clus
vv   AMP PEAK 27(20Q13.13) MUTATED AMP PEAK 27(20Q13.13) WILD-TYPE
  R0                            89                             185
  R1                             6                               8
  R2                             1                               0
  RX                             5                              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(20Q13.13) MUTATED                                  0    46
  AMP PEAK 27(20Q13.13) WILD-TYPE                                1    95
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20Q13.13) MUTATED                           4    52
  AMP PEAK 27(20Q13.13) WILD-TYPE                        11    93
D27V10, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       46
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       52
                                  clus
vv                                 AMP PEAK 27(20Q13.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         95
  BLACK OR AFRICAN AMERICAN                                     11
  WHITE                                                         93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.13) MUTATED     2  96
  AMP PEAK 27(20Q13.13) WILD-TYPE   6 191
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.13) MUTATED      2   96
  AMP PEAK 27(20Q13.13) WILD-TYPE    6  191
                        clus
vv                       AMP PEAK 27(20Q13.13) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            96
                        clus
vv                       AMP PEAK 27(20Q13.13) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             191
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(20Q13.33) MUTATION ANALYSIS
D28V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 28(20Q13.33) MUTATED    67  34
  AMP PEAK 28(20Q13.33) WILD-TYPE 133  58
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                            101                             191 
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                             34                              58 
$`AMP PEAK 28(20Q13.33) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10Y 
       10.78        10.59        48.99        37.32        10.13        23.34 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 
       13.84         0.26        14.60        13.45         0.66         0.39 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.10         0.13        79.73       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
        2.60         0.46        21.76        12.95        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND 
       29.16        21.14       102.74        13.78        30.61        73.38 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73F TCGA-DD-A73G 
       29.56        73.81         0.30        78.84        27.72       100.96 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACQ 
        0.53        59.18        55.40        53.19        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADA 
       48.49         5.59         5.62         4.50        22.09        30.58 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU 
       28.41         3.78        17.33         3.02         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEA 
        6.67         9.86         9.86         4.64        12.69        14.79 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVR TCGA-ED-A66X TCGA-ED-A66Y 
       15.65        15.65        35.08        72.26        13.35         0.23 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20        13.41         0.20         0.20        11.74        10.98 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3R2 TCGA-FV-A4ZQ 
        9.96        22.85        32.45        23.97         6.38         0.39 
TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 
        1.22        30.74        58.49        17.10        12.03         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
       11.80         2.14         2.66        11.84        13.38        12.72 
TCGA-MI-A75G TCGA-PD-A5DF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME 
       18.38        21.01        24.13        14.96        17.29        15.98 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZS-A9CD 
        8.32         0.99         4.01        13.55        45.57 

$`AMP PEAK 28(20Q13.33) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
        7.10         0.66        27.91        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        44.42 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 
       22.36         9.50        12.72         7.46         4.80         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A114 
        2.86         3.39         4.24         3.32         0.07        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       83.57        53.33        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65         6.71         6.02        18.35        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       17.59        20.12       107.11         0.36        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
      108.76        12.26        80.75        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD 
       10.98         1.45        13.48        11.41        65.75        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AAD2 
        1.91        58.16        40.77        38.04        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI 
       33.83        34.09        31.53        29.26        13.97        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ 
       24.00        24.13        20.91         0.39         3.95         5.29 
TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 
       57.27         9.67         9.63         9.47         8.52        12.56 
TCGA-DD-AAE8 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAVP TCGA-DD-AAVQ 
       11.31        12.16        15.45        16.37        79.07        79.10 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A97K 
       13.91         0.20         0.20         0.20        13.15         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       18.74        19.99         0.62        11.93        14.40        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         8.12         0.13         0.03         0.33        60.36 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       51.06        53.79        28.27        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       20.42         7.76         5.98        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 
        9.17         0.89         3.02         1.02         2.20        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC 
       20.75        17.06         4.01         2.14        24.36         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        4.27         9.57        16.67        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       58.88        16.37         4.44         2.04        21.04        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V 
       15.39        15.52        14.40         1.71         7.04         4.57 
TCGA-WJ-A86L TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
        1.02         4.67        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        35.05        74.24         8.22 

  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                           0.10                            0.03 
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                         113.00                          108.76 
  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE 
                          13.41                           15.52 
[1] "0.1 - 113.0 (13.4)" "0.0 - 108.8 (15.5)"
[1] "hr=" "1.2"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  AMP PEAK 28(20Q13.33) MUTATED        45       25         2         24
  AMP PEAK 28(20Q13.33) WILD-TYPE     101       47         0         28
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 28(20Q13.33) MUTATED            5          2        2         1
  AMP PEAK 28(20Q13.33) WILD-TYPE          2          5        0         0
                                 vv
clus                              STAGE IVB
  AMP PEAK 28(20Q13.33) MUTATED           1
  AMP PEAK 28(20Q13.33) WILD-TYPE         1
D28V3, multiclass
            clus
vv           AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  STAGE I                               45                             101
  STAGE II                              25                              47
  STAGE III                              2                               0
  STAGE IIIA                            24                              28
  STAGE IIIB                             5                               2
  STAGE IIIC                             2                               5
  STAGE IV                               2                               0
  STAGE IVA                              1                               0
  STAGE IVB                              1                               1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 28(20Q13.33) MUTATED      47  27  32   5
  AMP PEAK 28(20Q13.33) WILD-TYPE   108  51  32   7
D28V4, multiclass
       clus
vv      AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  T0+T1                            47                             108
  T2                               27                              51
  T3                               32                              32
  T4                                5                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED    83   2
  AMP PEAK 28(20Q13.33) WILD-TYPE 139   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED     83    2
  AMP PEAK 28(20Q13.33) WILD-TYPE  139    1
   clus
vv  AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  0                            83                             139
  1                             2                               1
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  AMP PEAK 28(20Q13.33) MUTATED    90   3  18
  AMP PEAK 28(20Q13.33) WILD-TYPE 148   1  51
D28V6, multiclass
    clus
vv   AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  M0                            90                             148
  M1                             3                               1
  MX                            18                              51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED    44  67
  AMP PEAK 28(20Q13.33) WILD-TYPE  56 144
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED     44   67
  AMP PEAK 28(20Q13.33) WILD-TYPE   56  144
        clus
vv       AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  FEMALE                            44                              56
  MALE                              67                             144
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  AMP PEAK 28(20Q13.33) MUTATED                         0
  AMP PEAK 28(20Q13.33) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  AMP PEAK 28(20Q13.33) MUTATED                        109
  AMP PEAK 28(20Q13.33) WILD-TYPE                      194
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 28(20Q13.33) MUTATED                                  2
  AMP PEAK 28(20Q13.33) WILD-TYPE                                4
D28V8, multiclass
                                  clus
vv                                 AMP PEAK 28(20Q13.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                   109
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             2
                                  clus
vv                                 AMP PEAK 28(20Q13.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     194
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               4
[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"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 28(20Q13.33) MUTATED    97   5   1   6
  AMP PEAK 28(20Q13.33) WILD-TYPE 177   9   0  10
D28V9, multiclass
    clus
vv   AMP PEAK 28(20Q13.33) MUTATED AMP PEAK 28(20Q13.33) WILD-TYPE
  R0                            97                             177
  R1                             5                               9
  R2                             1                               0
  RX                             6                              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(20Q13.33) MUTATED                                  0    51
  AMP PEAK 28(20Q13.33) WILD-TYPE                                1    90
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(20Q13.33) MUTATED                           4    54
  AMP PEAK 28(20Q13.33) WILD-TYPE                        11    91
D28V10, multiclass
                                  clus
vv                                 AMP PEAK 28(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       54
                                  clus
vv                                 AMP PEAK 28(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         90
  BLACK OR AFRICAN AMERICAN                                     11
  WHITE                                                         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"
D28V11, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q13.33) MUTATED     3 102
  AMP PEAK 28(20Q13.33) WILD-TYPE   5 185
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q13.33) MUTATED      3  102
  AMP PEAK 28(20Q13.33) WILD-TYPE    5  185
                        clus
vv                       AMP PEAK 28(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           102
                        clus
vv                       AMP PEAK 28(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             185
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(XQ28) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 29(XQ28) MUTATED    49  16
  AMP PEAK 29(XQ28) WILD-TYPE 151  76
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         65                         227 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         16                          76 
$`AMP PEAK 29(XQ28) MUTATED`
TCGA-BC-A10U TCGA-BC-A69I TCGA-BW-A5NO TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A11A 
       27.52        12.72         0.66         0.07        37.78         2.60 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF TCGA-DD-A4NK 
       21.14         5.62        17.59        13.78        30.97        39.78 
TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACS 
       78.84        10.98       100.96        53.19        60.10        48.49 
TCGA-DD-AAD2 TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE3 
       21.63        17.33         3.02         8.28         6.67         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVY 
        8.52        12.69        15.65        79.07        79.10        58.78 
TCGA-DD-AAW2 TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A3JL 
       49.48         0.23         0.20        18.74        11.74         9.96 
TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A3CG 
       22.85        19.10         0.33         0.39        53.79        22.13 
TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV0 TCGA-G3-AAV2 
       19.53        14.70        20.42         7.76         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K8 
        9.17         3.02         2.66        37.71         4.01        24.36 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-NI-A4U2 TCGA-O8-A75V 
       12.72         9.57        16.67        18.38        58.88         4.44 
TCGA-UB-A7ME TCGA-WQ-A9G7 TCGA-ZP-A9CV TCGA-ZS-A9CD TCGA-ZS-A9CG 
       15.98         0.99         4.67        45.57         8.22 

$`AMP PEAK 29(XQ28) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP 
        0.26        22.36         9.50        14.60         7.46        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.80         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
        3.32         0.10         0.10         0.13        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        55.69        19.76        25.81         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL 
       32.52        73.38        30.15        26.83        30.51        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
       10.98         9.30         7.56         1.45        27.72        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        65.75        59.18        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL 
       63.48        12.00        15.42         6.41         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       58.16        13.15        14.33        40.77        38.04         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62         4.50        18.54        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       31.53        30.58        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP 
       25.08        24.00        24.13        20.91         0.39         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
        5.29        57.27         7.10         9.67         9.86         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
        9.47         4.64        12.56        11.31        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS 
       15.45        16.37        15.65        35.08        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 
       61.87        61.38        56.48        55.86        54.05        47.70 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20         0.20        13.15        13.41         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        19.99        10.98         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        23.97        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.03        60.36         1.22        51.06        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       58.49        14.86        21.53        25.64         5.92        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       11.97        17.10        12.03         5.98         1.84        11.24 
TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RF 
       11.80         0.89         2.14         1.02         2.20        20.75 
TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06         2.14        11.84        13.38         5.92         4.27 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 
       12.85        20.71        10.85        16.37        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       17.29        14.40         1.71         7.04         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        1.02         4.01        13.55        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        35.05        74.24 

  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                       0.07                        0.03 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                     100.96                      113.00 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                       14.7                        14.4 
[1] "0.1 - 101.0 (14.7)" "0.0 - 113.0 (14.4)"
[1] "hr=" "1.3"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(XQ28) MUTATED        35       17         0         11          3
  AMP PEAK 29(XQ28) WILD-TYPE     111       55         2         41          4
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 29(XQ28) MUTATED            1        0         0         0
  AMP PEAK 29(XQ28) WILD-TYPE          6        2         1         2
D29V3, multiclass
            clus
vv           AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  STAGE I                           35                         111
  STAGE II                          17                          55
  STAGE III                          0                           2
  STAGE IIIA                        11                          41
  STAGE IIIB                         3                           4
  STAGE IIIC                         1                           6
  STAGE IV                           0                           2
  STAGE IVA                          0                           1
  STAGE IVB                          0                           2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  AMP PEAK 29(XQ28) MUTATED      36  18  14   2
  AMP PEAK 29(XQ28) WILD-TYPE   119  60  50  10
D29V4, multiclass
       clus
vv      AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  T0+T1                        36                         119
  T2                           18                          60
  T3                           14                          50
  T4                            2                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    45   0
  AMP PEAK 29(XQ28) WILD-TYPE 177   3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     45    0
  AMP PEAK 29(XQ28) WILD-TYPE  177    3
   clus
vv  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  0                        45                         177
  1                         0                           3
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 29(XQ28) MUTATED    55   0  16
  AMP PEAK 29(XQ28) WILD-TYPE 183   4  53
D29V6, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  M0                        55                         183
  M1                         0                           4
  MX                        16                          53
[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"
D29V7, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    12  59
  AMP PEAK 29(XQ28) WILD-TYPE  88 152
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     12   59
  AMP PEAK 29(XQ28) WILD-TYPE   88  152
        clus
vv       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  FEMALE                        12                          88
  MALE                          59                         152
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AMP PEAK 29(XQ28) MUTATED                         0                       71
  AMP PEAK 29(XQ28) WILD-TYPE                       2                      232
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  AMP PEAK 29(XQ28) MUTATED                                  0
  AMP PEAK 29(XQ28) WILD-TYPE                                6
D29V8, multiclass
                                  clus
vv                                 AMP PEAK 29(XQ28) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                71
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         0
                                  clus
vv                                 AMP PEAK 29(XQ28) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 232
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           6
[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"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 29(XQ28) MUTATED    63   3   0   4
  AMP PEAK 29(XQ28) WILD-TYPE 211  11   1  12
D29V9, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  R0                        63                         211
  R1                         3                          11
  R2                         0                           1
  RX                         4                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 29(XQ28) MUTATED                                  1    32
  AMP PEAK 29(XQ28) WILD-TYPE                                0   109
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(XQ28) MUTATED                           4    29
  AMP PEAK 29(XQ28) WILD-TYPE                        11   116
D29V10, multiclass
                                  clus
vv                                 AMP PEAK 29(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   32
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   29
                                  clus
vv                                 AMP PEAK 29(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                    109
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED     1  65
  AMP PEAK 29(XQ28) WILD-TYPE   7 222
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED      1   65
  AMP PEAK 29(XQ28) WILD-TYPE    7  222
                        clus
vv                       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             1                           7
  NOT HISPANIC OR LATINO                        65                         222
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    90  47
  DEL PEAK  1(1P36.31) WILD-TYPE 110  45
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                           137                            155 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            47                             45 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
       10.78        10.59        37.32        46.78        27.52         2.99 
TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5261 
       23.34        13.84        14.60         4.80         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A116 
        3.39         4.24         0.07         0.10        79.73        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
       90.71        66.31        12.95        45.11        49.15        29.16 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NH 
       55.69        19.76        25.81         7.66        30.61        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A73A 
       26.83        30.51        29.56        73.81         0.30        10.98 
TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA 
        9.30        27.72       100.96        13.48         0.53        65.75 
TCGA-DD-AACC TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACP TCGA-DD-AACW 
       55.40         6.41        60.10         0.30        13.15        38.04 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB 
        4.50        18.54        34.09        22.09        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       13.97        28.41         3.78        25.08        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW 
        0.39        17.33         3.02         3.95        57.27         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAEH 
        9.67         9.86         9.63         9.47         9.86        15.65 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 
       35.08        79.10        59.93        61.38        55.86        54.05 
TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E 
       12.69        13.35         0.23         0.20         0.20        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
        0.20         0.20         0.20        10.98         0.62        11.93 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       22.85        32.45        23.97        19.10        27.88         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.33        60.36         1.22        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M9 
       58.49        14.86        14.70        20.42        17.10         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75G 
       11.80         2.14        11.84        13.38         5.92        18.38 
TCGA-MI-A75H TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       12.85         4.44        21.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 
       14.96        14.40        15.98         7.04         8.32         0.99 
TCGA-WQ-AB4B TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        4.01        25.71        23.21         0.69        35.05 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U 
        7.10         0.66        48.99        27.91        10.13        27.52 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF 
       25.32         1.12        69.57         5.03        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36         9.50        12.72         7.46        13.45         0.66 
TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        0.07         3.32         0.10         0.13        37.78        83.57 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EK 
       79.40        19.79        75.65         6.71         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       13.64        21.14         5.62        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       73.38        30.97        39.78        56.25       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC9 
       80.75        78.84         7.56        10.98         1.45        11.41 
TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI 
       59.18        12.53        63.48        12.00        15.42        53.19 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX 
        1.91        58.16        14.33        48.49        40.77         5.59 
TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADL TCGA-DD-AADQ 
        5.62        21.63        33.83        31.53        20.91         5.29 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        7.10         8.28         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       12.69        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW2 
       79.07        72.26        61.87        56.48        58.78        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PZ TCGA-ED-A7XO 
       47.70        13.41        15.85        13.91         0.20         0.20 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HT 
       13.15        18.74        19.99        11.74         9.96        14.40 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Z 
        8.12         6.38         0.39        51.06        53.79        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.53        19.23        11.97 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
        7.76        12.03         5.98        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.17         0.89         3.02         1.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 
       37.71        20.75        17.06         4.01         2.14        24.36 
TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A8JO 
       12.72         4.27         9.57        16.67        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-UB-A7MB 
       58.88        16.37        21.01         2.04        19.04        17.29 
TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D0 
        1.71         4.57         1.02        13.55         4.67        23.57 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        74.24         8.22 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        113.00                         108.76 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         14.86                          13.91 
[1] "0.0 - 113.0 (14.9)" "0.1 - 108.8 (13.9)"
[1] "hr=" "1.3"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  1(1P36.31) MUTATED        66       35         1         23
  DEL PEAK  1(1P36.31) WILD-TYPE      80       37         1         29
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  1(1P36.31) MUTATED            3          4        2         1
  DEL PEAK  1(1P36.31) WILD-TYPE          4          3        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK  1(1P36.31) MUTATED           1
  DEL PEAK  1(1P36.31) WILD-TYPE         1
D30V3, multiclass
            clus
vv           DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                              66                             80
  STAGE II                             35                             37
  STAGE III                             1                              1
  STAGE IIIA                           23                             29
  STAGE IIIB                            3                              4
  STAGE IIIC                            4                              3
  STAGE IV                              2                              0
  STAGE IVA                             1                              0
  STAGE IVB                             1                              1
[1] 9 2
[1] 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      71 37 30  7
  DEL PEAK  1(1P36.31) WILD-TYPE    84 41 34  5
D30V4, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T0+T1                           71                             84
  T2                              37                             41
  T3                              30                             34
  T4                               7                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED   104   2
  DEL PEAK  1(1P36.31) WILD-TYPE 118   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED    104    2
  DEL PEAK  1(1P36.31) WILD-TYPE  118    1
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                          104                            118
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK  1(1P36.31) MUTATED   117   3  26
  DEL PEAK  1(1P36.31) WILD-TYPE 121   1  43
D30V6, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  M0                          117                            121
  M1                            3                              1
  MX                           26                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    53  93
  DEL PEAK  1(1P36.31) WILD-TYPE  47 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     53   93
  DEL PEAK  1(1P36.31) WILD-TYPE   47  118
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           53                             47
  MALE                             93                            118
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK  1(1P36.31) MUTATED                         0
  DEL PEAK  1(1P36.31) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK  1(1P36.31) MUTATED                        141
  DEL PEAK  1(1P36.31) WILD-TYPE                      162
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  1(1P36.31) MUTATED                                  5
  DEL PEAK  1(1P36.31) WILD-TYPE                                1
D30V8, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  141
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            5
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    162
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              1
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.31) MUTATED   127   9   1   7
  DEL PEAK  1(1P36.31) WILD-TYPE 147   5   0   9
D30V9, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  R0                          127                            147
  R1                            9                              5
  R2                            1                              0
  RX                            7                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.31) MUTATED                                  0    73
  DEL PEAK  1(1P36.31) WILD-TYPE                                1    68
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED                           3    66
  DEL PEAK  1(1P36.31) WILD-TYPE                        12    79
D30V10, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      73
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      66
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        68
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                        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"
D30V11, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     4 136
  DEL PEAK  1(1P36.31) WILD-TYPE   4 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      4  136
  DEL PEAK  1(1P36.31) WILD-TYPE    4  151
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            151
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  2(1P36.11) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  2(1P36.11) MUTATED    79  37
  DEL PEAK  2(1P36.11) WILD-TYPE 121  55
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           116                            176 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            37                             55 
$`DEL PEAK  2(1P36.11) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
       10.78        10.59        37.32        46.78        27.52         2.99 
TCGA-BC-A112 TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        5.03        14.60         4.80         0.07         2.86         0.39 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.07         0.10        79.73        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EH 
        2.60         0.46        21.76        90.71        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A9 TCGA-DD-A4NA 
       29.16        21.14        55.69         7.66        30.61        33.14 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B 
       30.15        26.83        30.51        29.56        73.81         9.30 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACJ 
       27.72       100.96         0.53        65.75        55.40        60.10 
TCGA-DD-AACK TCGA-DD-AACP TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD5 
        0.30        13.15        38.04         4.50        18.54        34.09 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ 
       22.09        30.58        29.26        13.97        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW 
       24.13         0.39         3.02         3.95        57.27         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEK 
        9.67         9.86         9.63         9.86        16.37        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 
       79.10        59.93        61.87        61.38        55.86        54.05 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 
       13.41        13.35         0.23         0.20        13.41         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS 
        0.20         0.20        10.98         0.62        11.93        22.85 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP 
       32.45        23.97        27.88         0.13         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A5SL 
        1.22        30.74        58.49        14.86        14.70        20.42 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K7 
       17.10         1.84        11.80         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       12.72         5.92        18.38        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       14.96        14.40         7.04         8.32         0.99         4.01 
TCGA-ZP-A9CZ TCGA-ZP-A9D1 
       23.21         0.69 

$`DEL PEAK  2(1P36.11) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U 
        7.10         0.66        48.99        27.91        10.13        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
        0.26        22.36         9.50        12.72         7.46        13.45 
TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC 
        0.66         3.39         4.24         3.32         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       37.78        83.57        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       75.65         6.71        12.95         6.02        18.35        13.64 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76        25.81        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND 
      102.74       107.11        13.78         0.36        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.97        39.78        56.25       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        10.98         7.56        10.98         1.45 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       13.48        11.41        59.18        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
       15.42         6.41        53.19         1.91        58.16        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 
       48.49        40.77         5.59         5.62        21.63        33.83 
TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADQ 
       31.53        28.41         3.78        20.91        17.33         5.29 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        7.10         8.28         9.47         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG 
       11.31        12.69        14.79        12.16        15.45        15.65 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW2 
       15.65        79.07        72.26        56.48        58.78        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ 
       47.70        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        0.20        13.15        18.74        19.99        11.74         9.96 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZQ 
       14.40        19.10         8.12         6.38         0.03         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       51.06        53.79        28.27        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M6 
        5.92        19.53        19.23        11.97         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        5.98        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C 
       17.06         4.01         2.14        24.36         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       16.67        12.85        20.71        10.85        58.88        16.37 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MB 
        4.44        21.01         2.04        21.04        19.04        17.29 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV 
        1.71        15.98         4.57         1.02        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       25.71        23.57        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                        113.00                         108.76 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                        14.910                         13.875 
[1] "0.1 - 113.0 (14.9)" "0.0 - 108.8 (13.9)"
[1] "hr=" "1"  
D31V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  2(1P36.11) MUTATED        50       34         1         22
  DEL PEAK  2(1P36.11) WILD-TYPE      96       38         1         30
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  2(1P36.11) MUTATED            3          4        2         1
  DEL PEAK  2(1P36.11) WILD-TYPE          4          3        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK  2(1P36.11) MUTATED           1
  DEL PEAK  2(1P36.11) WILD-TYPE         1
D31V3, multiclass
            clus
vv           DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  STAGE I                              50                             96
  STAGE II                             34                             38
  STAGE III                             1                              1
  STAGE IIIA                           22                             30
  STAGE IIIB                            3                              4
  STAGE IIIC                            4                              3
  STAGE IV                              2                              0
  STAGE IVA                             1                              0
  STAGE IVB                             1                              1
[1] 9 2
[1] 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(1P36.11) MUTATED      54  37  30   5
  DEL PEAK  2(1P36.11) WILD-TYPE   101  41  34   7
D31V4, multiclass
       clus
vv      DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  T0+T1                           54                            101
  T2                              37                             41
  T3                              30                             34
  T4                               5                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED    92   3
  DEL PEAK  2(1P36.11) WILD-TYPE 130   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED     92    3
  DEL PEAK  2(1P36.11) WILD-TYPE  130    0
   clus
vv  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  0                           92                            130
  1                            3                              0
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK  2(1P36.11) MUTATED   104   3  19
  DEL PEAK  2(1P36.11) WILD-TYPE 134   1  50
D31V6, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  M0                          104                            134
  M1                            3                              1
  MX                           19                             50
[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"
D31V7, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED    43  83
  DEL PEAK  2(1P36.11) WILD-TYPE  57 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED     43   83
  DEL PEAK  2(1P36.11) WILD-TYPE   57  128
        clus
vv       DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  FEMALE                           43                             57
  MALE                             83                            128
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                         0
  DEL PEAK  2(1P36.11) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                        122
  DEL PEAK  2(1P36.11) WILD-TYPE                      181
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  2(1P36.11) MUTATED                                  4
  DEL PEAK  2(1P36.11) WILD-TYPE                                2
D31V8, multiclass
                                  clus
vv                                 DEL PEAK  2(1P36.11) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  122
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK  2(1P36.11) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    181
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              2
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  2(1P36.11) MUTATED   110   8   1   6
  DEL PEAK  2(1P36.11) WILD-TYPE 164   6   0  10
D31V9, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  R0                          110                            164
  R1                            8                              6
  R2                            1                              0
  RX                            6                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P36.11) MUTATED                                  0    66
  DEL PEAK  2(1P36.11) WILD-TYPE                                1    75
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P36.11) MUTATED                           3    56
  DEL PEAK  2(1P36.11) WILD-TYPE                        12    89
D31V10, multiclass
                                  clus
vv                                 DEL PEAK  2(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      66
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      56
                                  clus
vv                                 DEL PEAK  2(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        75
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                        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"
D31V11, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED     3 120
  DEL PEAK  2(1P36.11) WILD-TYPE   5 167
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED      3  120
  DEL PEAK  2(1P36.11) WILD-TYPE    5  167
                        clus
vv                       DEL PEAK  2(1P36.11) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       DEL PEAK  2(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            167
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    23  13
  DEL PEAK  3(2Q22.1) WILD-TYPE 177  79
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           36                           256 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           13                            79 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-BC-A10R TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BD-A3EP 
        7.10        10.78        10.13        23.34         0.26        13.45 
TCGA-DD-A115 TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A4NJ 
       83.57        13.64        21.14         5.62         7.66        30.51 
TCGA-DD-A73B TCGA-DD-AACE TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AADI TCGA-DD-AADL 
        9.30        63.48        40.77         5.62        25.08        20.91 
TCGA-DD-AADN TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAED 
       17.33         6.67         9.47         8.52         4.64        15.45 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-FV-A3I1 TCGA-G3-AAV7 
       13.41         0.23         0.20         0.20         8.12         3.02 
TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-ZP-A9D2 
        2.20        11.84        15.39         7.04         4.01        24.43 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
       10.59         0.66        48.99        27.91        37.32        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 
       27.52        27.52         2.99        25.32         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        44.42        13.84        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72         7.46         4.80         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.39         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        79.73        37.78        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X 
       45.11        49.15         6.02        29.16        18.35        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        30.97        30.15        26.83        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        10.98         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      100.96        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       48.49        38.04         5.59         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       33.83        34.09        22.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       13.97        28.41         3.78        24.00        24.13         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        3.02         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.67         9.86         9.63         9.86        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       12.69        14.79        12.16        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       47.70        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        13.15        13.41         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 
       11.80         9.70         9.17         0.89         2.14         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 
       15.98         8.32         4.57         1.02         0.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57         0.69        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         0.20                          0.03 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        83.57                        113.00 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         9.80                         15.47 
[1] "0.2 - 83.6 (9.8)"   "0.0 - 113.0 (15.5)"
[1] "hr=" "1.8"
D32V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  3(2Q22.1) MUTATED        18       13         0          8
  DEL PEAK  3(2Q22.1) WILD-TYPE     128       59         2         44
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  3(2Q22.1) MUTATED            0          0        0         0
  DEL PEAK  3(2Q22.1) WILD-TYPE          7          7        2         1
                               vv
clus                            STAGE IVB
  DEL PEAK  3(2Q22.1) MUTATED           0
  DEL PEAK  3(2Q22.1) WILD-TYPE         2
D32V3, multiclass
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                             18                           128
  STAGE II                            13                            59
  STAGE III                            0                             2
  STAGE IIIA                           8                            44
  STAGE IIIB                           0                             7
  STAGE IIIC                           0                             7
  STAGE IV                             0                             2
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] 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(2Q22.1) MUTATED      18  14   9   1
  DEL PEAK  3(2Q22.1) WILD-TYPE   137  64  55  11
D32V4, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T0+T1                          18                           137
  T2                             14                            64
  T3                              9                            55
  T4                              1                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    30   0
  DEL PEAK  3(2Q22.1) WILD-TYPE 192   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     30    0
  DEL PEAK  3(2Q22.1) WILD-TYPE  192    3
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          30                           192
  1                           0                             3
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  3(2Q22.1) MUTATED    33   0   9
  DEL PEAK  3(2Q22.1) WILD-TYPE 205   4  60
D32V6, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  M0                          33                           205
  M1                           0                             4
  MX                           9                            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    11  31
  DEL PEAK  3(2Q22.1) WILD-TYPE  89 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     11   31
  DEL PEAK  3(2Q22.1) WILD-TYPE   89  180
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          11                            89
  MALE                            31                           180
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                         0
  DEL PEAK  3(2Q22.1) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                         41
  DEL PEAK  3(2Q22.1) WILD-TYPE                      262
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  3(2Q22.1) MUTATED                                  1
  DEL PEAK  3(2Q22.1) WILD-TYPE                                5
D32V8, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  41
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   262
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             5
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2Q22.1) MUTATED    40   0   0   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 234  14   1  14
D32V9, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  R0                          40                           234
  R1                           0                            14
  R2                           0                             1
  RX                           2                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2Q22.1) MUTATED                                  0    23
  DEL PEAK  3(2Q22.1) WILD-TYPE                                1   118
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED                           2    16
  DEL PEAK  3(2Q22.1) WILD-TYPE                        13   129
D32V10, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     23
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     16
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      118
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     1  37
  DEL PEAK  3(2Q22.1) WILD-TYPE   7 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      1   37
  DEL PEAK  3(2Q22.1) WILD-TYPE    7  250
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           250
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    34  16
  DEL PEAK  4(2Q37.3) WILD-TYPE 166  76
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           50                           242 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           16                            76 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BD-A3EP 
       10.78        23.34        44.42         0.26         9.50        13.45 
TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C 
        0.66         0.10        79.73        83.57         2.60        21.76 
TCGA-DD-A1EB TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A4NA TCGA-DD-A4NJ 
       66.31        13.64         5.62        19.76        33.14        30.51 
TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AACE TCGA-DD-AACU TCGA-DD-AAD5 TCGA-DD-AADC 
       12.26         9.30        63.48        40.77        34.09        13.97 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AAED 
        3.78        25.08        20.91        17.33         3.95        15.45 
TCGA-DD-AAEG TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       15.65        13.41         0.23         0.20         0.20         0.20 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAV7 
       27.88         8.12         0.33        14.70         1.84         3.02 
TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB 
        2.20        11.84        15.39        15.52        14.96        17.29 
TCGA-UB-A7MF TCGA-WQ-AB4B 
        7.04         4.01 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        69.57         5.03        13.84        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       12.72         7.46         4.80         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       37.78        53.33       113.00         7.33         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       90.71        79.40        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       45.11        49.15         6.02        29.16        18.35        21.14 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        30.97        30.15        26.83        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       10.98         7.56        10.98         1.45        27.72       100.96 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        12.00        15.42         6.41        53.19        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         1.91        58.16        13.15        14.33        48.49 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD 
       33.83        22.09        31.53        30.58        29.26        28.41 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR 
       24.00        24.13         0.39         3.02         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
        7.10         8.28         6.67         9.67         9.86         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.47         9.86         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEK 
       12.69        14.79        12.16        16.37        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        79.10        72.26        59.93        61.87        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP 
       12.69        15.85        13.91        13.35         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        23.97        19.10         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10         7.76        12.03         5.98        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 
       11.80         9.70         9.17         0.89         2.14         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
       24.13        14.40         1.71        15.98         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        1.02         0.99        13.55         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        83.57                        113.00 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       13.545                        14.825 
[1] "0.1 - 83.6 (13.5)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1.3"
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  4(2Q37.3) MUTATED        23       17         0         11
  DEL PEAK  4(2Q37.3) WILD-TYPE     123       55         2         41
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  4(2Q37.3) MUTATED            1          1        0         0
  DEL PEAK  4(2Q37.3) WILD-TYPE          6          6        2         1
                               vv
clus                            STAGE IVB
  DEL PEAK  4(2Q37.3) MUTATED           0
  DEL PEAK  4(2Q37.3) WILD-TYPE         2
D33V3, multiclass
            clus
vv           DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                             23                           123
  STAGE II                            17                            55
  STAGE III                            0                             2
  STAGE IIIA                          11                            41
  STAGE IIIB                           1                             6
  STAGE IIIC                           1                             6
  STAGE IV                             0                             2
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] 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(2Q37.3) MUTATED      23  18  12   1
  DEL PEAK  4(2Q37.3) WILD-TYPE   132  60  52  11
D33V4, multiclass
       clus
vv      DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T0+T1                          23                           132
  T2                             18                            60
  T3                             12                            52
  T4                              1                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    36   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 186   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     36    1
  DEL PEAK  4(2Q37.3) WILD-TYPE  186    2
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          36                           186
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  4(2Q37.3) MUTATED    45   0   9
  DEL PEAK  4(2Q37.3) WILD-TYPE 193   4  60
D33V6, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  M0                          45                           193
  M1                           0                             4
  MX                           9                            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    18  36
  DEL PEAK  4(2Q37.3) WILD-TYPE  82 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     18   36
  DEL PEAK  4(2Q37.3) WILD-TYPE   82  175
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          18                            82
  MALE                            36                           175
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                         0
  DEL PEAK  4(2Q37.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  4(2Q37.3) MUTATED                         51
  DEL PEAK  4(2Q37.3) WILD-TYPE                      252
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  4(2Q37.3) MUTATED                                  3
  DEL PEAK  4(2Q37.3) WILD-TYPE                                3
D33V8, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  51
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   252
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q37.3) MUTATED    48   2   0   4
  DEL PEAK  4(2Q37.3) WILD-TYPE 226  12   1  12
D33V9, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  R0                          48                           226
  R1                           2                            12
  R2                           0                             1
  RX                           4                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.3) MUTATED                                  0    25
  DEL PEAK  4(2Q37.3) WILD-TYPE                                1   116
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           4    23
  DEL PEAK  4(2Q37.3) WILD-TYPE                        11   122
D33V10, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     25
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     23
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      116
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     2  46
  DEL PEAK  4(2Q37.3) WILD-TYPE   6 241
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      2   46
  DEL PEAK  4(2Q37.3) WILD-TYPE    6  241
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           241
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  5(3P13) MUTATION ANALYSIS
D34V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  5(3P13) MUTATED    37  16
  DEL PEAK  5(3P13) WILD-TYPE 163  76
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         53                         239 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                         16                          76 
$`DEL PEAK  5(3P13) MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 
       10.78         0.66        37.32        10.13         5.03        13.84 
TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A11A 
        2.86         4.24         0.07         0.10        79.73         2.60 
TCGA-DD-A1E9 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NO 
       90.71        30.61        33.14        30.15        26.83        73.81 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAD2 TCGA-DD-AADC TCGA-DD-AADJ TCGA-DD-AADO 
      100.96        13.48        21.63        13.97        24.00         3.02 
TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A66Y TCGA-ED-A7PX 
        9.67         9.86        79.10        61.87         0.23         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA TCGA-FV-A3I0 
        0.20         0.20        13.41         0.20        11.74        27.88 
TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 
        0.13        51.06        58.49        11.80         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-RC-A7SH TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
       13.38         5.92        15.39        14.40         1.71         7.04 
TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-ZS-A9CF 
        4.01        23.57         0.69        35.05        74.24 

$`DEL PEAK  5(3P13) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T 
        7.10        10.59        48.99        27.91        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42         0.26        22.36         9.50        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
        7.46        13.45         4.80         0.66         0.07         0.39 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        3.39         3.32         0.10         0.13        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK 
        0.36        32.52        73.38        30.97        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       27.72         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       29.26        28.41         3.78        25.08        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        17.33         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
        8.28         6.67         9.86         9.63         9.47         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       15.45        16.37        15.65        15.65        35.08        79.07 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.26        59.93        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 
       13.91        13.35         0.20        13.15         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       22.85        14.40        32.45        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
       11.24         8.55         9.70         9.17         0.89         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C 
        4.01         2.14        24.36        12.72         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U 
       15.52        24.13        14.96        17.29        15.98         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         1.02         0.99        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.21        24.43        12.99        45.57         8.22 

  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                       0.07                        0.03 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                     100.96                      113.00 
  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE 
                      11.84                       15.45 
[1] "0.1 - 101.0 (11.8)" "0.0 - 113.0 (15.4)"
[1] "hr=" "1"  
D34V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(3P13) MUTATED        17       18         0         15          2
  DEL PEAK  5(3P13) WILD-TYPE     129       54         2         37          5
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  5(3P13) MUTATED            3        1         0         1
  DEL PEAK  5(3P13) WILD-TYPE          4        1         1         1
D34V3, multiclass
            clus
vv           DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  STAGE I                           17                         129
  STAGE II                          18                          54
  STAGE III                          0                           2
  STAGE IIIA                        15                          37
  STAGE IIIB                         2                           5
  STAGE IIIC                         3                           4
  STAGE IV                           1                           1
  STAGE IVA                          0                           1
  STAGE IVB                          1                           1
[1] 9 2
[1] 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(3P13) MUTATED      19  21  18   4
  DEL PEAK  5(3P13) WILD-TYPE   136  57  46   8
D34V4, multiclass
       clus
vv      DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  T0+T1                        19                         136
  T2                           21                          57
  T3                           18                          46
  T4                            4                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED    43   1
  DEL PEAK  5(3P13) WILD-TYPE 179   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     43    1
  DEL PEAK  5(3P13) WILD-TYPE  179    2
   clus
vv  DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  0                        43                         179
  1                         1                           2
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK  5(3P13) MUTATED    46   2  14
  DEL PEAK  5(3P13) WILD-TYPE 192   2  55
D34V6, multiclass
    clus
vv   DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  M0                        46                         192
  M1                         2                           2
  MX                        14                          55
[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"
D34V7, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED    27  35
  DEL PEAK  5(3P13) WILD-TYPE  73 176
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED     27   35
  DEL PEAK  5(3P13) WILD-TYPE   73  176
        clus
vv       DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  FEMALE                        27                          73
  MALE                          35                         176
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK  5(3P13) MUTATED                         0                       57
  DEL PEAK  5(3P13) WILD-TYPE                       2                      246
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  5(3P13) MUTATED                                  5
  DEL PEAK  5(3P13) WILD-TYPE                                1
D34V8, multiclass
                                  clus
vv                                 DEL PEAK  5(3P13) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                                57
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         5
                                  clus
vv                                 DEL PEAK  5(3P13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 246
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           1
[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"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  5(3P13) MUTATED    58   1   0   3
  DEL PEAK  5(3P13) WILD-TYPE 216  13   1  13
D34V9, multiclass
    clus
vv   DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  R0                        58                         216
  R1                         1                          13
  R2                         0                           1
  RX                         3                          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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P13) MUTATED                                  0    30
  DEL PEAK  5(3P13) WILD-TYPE                                1   111
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P13) MUTATED                           3    29
  DEL PEAK  5(3P13) WILD-TYPE                        12   116
D34V10, multiclass
                                  clus
vv                                 DEL PEAK  5(3P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   30
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   29
                                  clus
vv                                 DEL PEAK  5(3P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                    111
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, binary
                             cls
clus                            0   1
  DEL PEAK  5(3P13) MUTATED     1  58
  DEL PEAK  5(3P13) WILD-TYPE   7 229
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(3P13) MUTATED      1   58
  DEL PEAK  5(3P13) WILD-TYPE    7  229
                        clus
vv                       DEL PEAK  5(3P13) MUTATED DEL PEAK  5(3P13) WILD-TYPE
  HISPANIC OR LATINO                             1                           7
  NOT HISPANIC OR LATINO                        58                         229
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  6(4P16.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4P16.3) MUTATED    39  23
  DEL PEAK  6(4P16.3) WILD-TYPE 161  69
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           62                           230 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           23                            69 
$`DEL PEAK  6(4P16.3) MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BC-A69H 
       10.78         0.66        23.34         5.03         9.50        14.60 
TCGA-BW-A5NO TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EI TCGA-DD-A1EJ 
        0.66         0.13        37.78         7.33         6.02        29.16 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A73A 
       55.69         5.62        26.83        30.51        29.56        10.98 
TCGA-DD-AAC8 TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACM TCGA-DD-AACP 
        0.53        63.48        12.00        15.42        58.16        13.15 
TCGA-DD-AACU TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AAE8 
       40.77        34.09        31.53        13.97        28.41        11.31 
TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7XO 
       15.45        35.08        79.10        61.87        13.41         0.20 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A4ZP TCGA-G3-A25S 
        0.20        10.98         0.62        23.97        60.36         1.22 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 
       53.79        58.49        25.64        11.24        11.80         0.89 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-PD-A5DF 
       37.71        17.06        11.84        13.38        18.38        21.01 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-YA-A8S7 
       24.13        14.40        15.98         7.04         4.01        13.55 
TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       24.43        35.05 

$`DEL PEAK  6(4P16.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
        7.10        10.59        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       46.78        27.52        27.52         2.99        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I 
       69.57        44.42        13.84         0.26        22.36        12.72 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        7.46        13.45         4.80         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK 
       75.65         6.71        12.95        45.11        49.15        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       27.72       100.96        13.48        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       55.40        12.53         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
        1.91        14.33        48.49        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA 
        4.50        18.54        21.63        33.83        22.09        30.58 
TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       29.26         3.78        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        17.33         3.02         3.95         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
        7.10         8.28         6.67         9.67         9.86         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 
        9.47         9.86         8.52         4.64        12.56        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP 
       14.79        12.16        16.37        15.65        15.65        79.07 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.26        59.93        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       54.05        49.48        47.70        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        51.06        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        8.55         9.70         9.17         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 
        2.20         2.66        20.75         4.01         2.14        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 
       20.71        10.85        58.88        16.37         4.44         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        19.04        15.39        15.52        14.96        17.29 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-ZP-A9CV 
        1.71         8.32         4.57         1.02         0.99         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57         0.69        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                         79.1                         113.0 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       15.010                        14.365 
[1] "0.1 - 79.1 (15.0)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1.4"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  6(4P16.3) MUTATED        28       18         0         17
  DEL PEAK  6(4P16.3) WILD-TYPE     118       54         2         35
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  6(4P16.3) MUTATED            1          2        2         1
  DEL PEAK  6(4P16.3) WILD-TYPE          6          5        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK  6(4P16.3) MUTATED           0
  DEL PEAK  6(4P16.3) WILD-TYPE         2
D35V3, multiclass
            clus
vv           DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  STAGE I                             28                           118
  STAGE II                            18                            54
  STAGE III                            0                             2
  STAGE IIIA                          17                            35
  STAGE IIIB                           1                             6
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            1                             0
  STAGE IVB                            0                             2
[1] 9 2
[1] 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      30  20  19   3
  DEL PEAK  6(4P16.3) WILD-TYPE   125  58  45   9
D35V4, multiclass
       clus
vv      DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  T0+T1                          30                           125
  T2                             20                            58
  T3                             19                            45
  T4                              3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    50   2
  DEL PEAK  6(4P16.3) WILD-TYPE 172   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     50    2
  DEL PEAK  6(4P16.3) WILD-TYPE  172    1
   clus
vv  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  0                          50                           172
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  6(4P16.3) MUTATED    56   2  15
  DEL PEAK  6(4P16.3) WILD-TYPE 182   2  54
D35V6, multiclass
    clus
vv   DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  M0                          56                           182
  M1                           2                             2
  MX                          15                            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED    16  57
  DEL PEAK  6(4P16.3) WILD-TYPE  84 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED     16   57
  DEL PEAK  6(4P16.3) WILD-TYPE   84  154
        clus
vv       DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          16                            84
  MALE                            57                           154
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  6(4P16.3) MUTATED                         0
  DEL PEAK  6(4P16.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  6(4P16.3) MUTATED                         71
  DEL PEAK  6(4P16.3) WILD-TYPE                      232
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  6(4P16.3) MUTATED                                  2
  DEL PEAK  6(4P16.3) WILD-TYPE                                4
D35V8, multiclass
                                  clus
vv                                 DEL PEAK  6(4P16.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  71
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK  6(4P16.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   232
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(4P16.3) MUTATED    64   3   1   4
  DEL PEAK  6(4P16.3) WILD-TYPE 210  11   0  12
D35V9, multiclass
    clus
vv   DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  R0                          64                           210
  R1                           3                            11
  R2                           1                             0
  RX                           4                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(4P16.3) MUTATED                                  0    38
  DEL PEAK  6(4P16.3) WILD-TYPE                                1   103
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4P16.3) MUTATED                           5    28
  DEL PEAK  6(4P16.3) WILD-TYPE                        10   117
D35V10, multiclass
                                  clus
vv                                 DEL PEAK  6(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     38
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     28
                                  clus
vv                                 DEL PEAK  6(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      103
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                      117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                               cls
clus                              0   1
  DEL PEAK  6(4P16.3) MUTATED     3  67
  DEL PEAK  6(4P16.3) WILD-TYPE   5 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED      3   67
  DEL PEAK  6(4P16.3) WILD-TYPE    5  220
                        clus
vv                       DEL PEAK  6(4P16.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          67
                        clus
vv                       DEL PEAK  6(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           220
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  7(4Q21.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q21.3) MUTATED    90  43
  DEL PEAK  7(4Q21.3) WILD-TYPE 110  49
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                          133                           159 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                           43                            49 
$`DEL PEAK  7(4Q21.3) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
       10.78        10.59         0.66        27.52        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H 
        1.12         5.03        13.84         0.26         9.50        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 
       13.45         0.66         0.07         0.39         4.24         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 
        0.10         0.13        79.73        37.78        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
        2.60        66.31        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A3A9 
       29.16        13.64        55.69         5.62       102.74        30.61 
TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
       73.38        30.15        26.83        30.51        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC 
       12.26         9.30       100.96         0.53        59.18        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       63.48        12.00        15.42         1.91        58.16        13.15 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 
       48.49        40.77        38.04         5.62        33.83        34.09 
TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADL 
       31.53        29.26        13.97        28.41        25.08        20.91 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
        3.02         3.95        57.27         9.67         9.86         9.63 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ 
        4.64        11.31        14.79        15.45        35.08        79.10 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 
       59.93        61.87        61.38        55.86        54.05        13.41 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         0.20         0.20         0.20         0.20        13.15 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A3I1 
        0.20         0.20        10.98         0.62        23.97         8.12 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        0.33        60.36         1.22        58.49        14.86        21.53 
TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       14.70        17.10         1.84         8.55        11.80         9.70 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RG 
        0.89         2.14         3.02         1.02        37.71        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G 
       11.84        13.38        24.36        12.72         5.92        18.38 
TCGA-O8-A75V TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC 
        4.44        15.39        15.52        24.13        17.29        14.40 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D2 
       15.98         7.04         0.99         4.01        13.55        24.43 
TCGA-ZS-A9CE 
       35.05 

$`DEL PEAK  7(4Q21.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        7.10        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I 
        2.99        25.32        69.57        44.42        22.36        12.72 
TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA 
        7.46         4.80         2.86         3.39         3.32         0.07 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       83.57       113.00         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK TCGA-DD-A39V 
       79.40        19.79        75.65         6.71        18.35        21.14 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78         0.36        33.14        32.52        30.97 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       39.78        56.25       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
       10.98         7.56        10.98         1.45        27.72        13.48 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       11.41        65.75        12.53         6.41        53.19        60.10 
TCGA-DD-AACK TCGA-DD-AACQ TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        0.30        14.33         5.59         4.50        18.54        21.63 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       22.09        30.58         3.78        24.00        24.13         0.39 
TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE2 
       17.33         5.29         7.10         8.28         6.67         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE 
        9.86         8.52        12.56        12.69        12.16        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY 
       15.65        15.65        79.07        72.26        56.48        58.78 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       49.48        47.70        12.69        15.85        13.91         0.23 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
       13.41         0.20        18.74        19.99        11.74         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        6.38         0.13         0.03         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        30.74        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.23        11.97        20.42         7.76        12.03         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV3 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 
       11.24         9.17         2.20         2.66        20.75         4.01 
TCGA-KR-A7K0 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
        2.14         4.27         9.57        16.67        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88        16.37        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       19.04        14.96         1.71         8.32         4.57         1.02 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57         0.69        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        74.24         8.22 

  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                       102.74                        113.00 
  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE 
                        13.84                         15.65 
[1] "0.1 - 102.7 (13.8)" "0.0 - 113.0 (15.7)"
[1] "hr=" "1.1"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  7(4Q21.3) MUTATED        67       38         2         25
  DEL PEAK  7(4Q21.3) WILD-TYPE      79       34         0         27
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  7(4Q21.3) MUTATED            3          2        2         1
  DEL PEAK  7(4Q21.3) WILD-TYPE          4          5        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK  7(4Q21.3) MUTATED           1
  DEL PEAK  7(4Q21.3) WILD-TYPE         1
D36V3, multiclass
            clus
vv           DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  STAGE I                             67                            79
  STAGE II                            38                            34
  STAGE III                            2                             0
  STAGE IIIA                          25                            27
  STAGE IIIB                           3                             4
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            1                             0
  STAGE IVB                            1                             1
[1] 9 2
[1] 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(4Q21.3) MUTATED      69 41 32  5
  DEL PEAK  7(4Q21.3) WILD-TYPE    86 37 32  7
D36V4, multiclass
       clus
vv      DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  T0+T1                          69                            86
  T2                             41                            37
  T3                             32                            32
  T4                              5                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED   109   2
  DEL PEAK  7(4Q21.3) WILD-TYPE 113   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED    109    2
  DEL PEAK  7(4Q21.3) WILD-TYPE  113    1
   clus
vv  DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  0                         109                           113
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  7(4Q21.3) MUTATED   122   3  23
  DEL PEAK  7(4Q21.3) WILD-TYPE 116   1  46
D36V6, multiclass
    clus
vv   DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  M0                         122                           116
  M1                           3                             1
  MX                          23                            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED    45 103
  DEL PEAK  7(4Q21.3) WILD-TYPE  55 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED     45  103
  DEL PEAK  7(4Q21.3) WILD-TYPE   55  108
        clus
vv       DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  FEMALE                          45                            55
  MALE                           103                           108
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  7(4Q21.3) MUTATED                         0
  DEL PEAK  7(4Q21.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  7(4Q21.3) MUTATED                        145
  DEL PEAK  7(4Q21.3) WILD-TYPE                      158
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  7(4Q21.3) MUTATED                                  3
  DEL PEAK  7(4Q21.3) WILD-TYPE                                3
D36V8, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 145
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  7(4Q21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   158
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(4Q21.3) MUTATED   133   6   1   8
  DEL PEAK  7(4Q21.3) WILD-TYPE 141   8   0   8
D36V9, multiclass
    clus
vv   DEL PEAK  7(4Q21.3) MUTATED DEL PEAK  7(4Q21.3) WILD-TYPE
  R0                         133                           141
  R1                           6                             8
  R2                           1                             0
  RX                           8                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(4Q21.3) MUTATED                                  0    81
  DEL PEAK  7(4Q21.3) WILD-TYPE                                1    60
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q21.3) MUTATED                           8    55
  DEL PEAK  7(4Q21.3) WILD-TYPE                         7    90
D36V10, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     81
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     55
                                  clus
vv                                 DEL PEAK  7(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       60
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       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"
D36V11, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q21.3) MUTATED     5 136
  DEL PEAK  7(4Q21.3) WILD-TYPE   3 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q21.3) MUTATED      5  136
  DEL PEAK  7(4Q21.3) WILD-TYPE    3  151
                        clus
vv                       DEL PEAK  7(4Q21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         136
                        clus
vv                       DEL PEAK  7(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           151
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  8(4Q22.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q22.3) MUTATED    91  43
  DEL PEAK  8(4Q22.3) WILD-TYPE 109  49
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                          134                           158 
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                           43                            49 
$`DEL PEAK  8(4Q22.3) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
       10.78        10.59         0.66        27.52        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H 
        1.12         5.03        13.84         0.26         9.50        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 
       13.45         0.66         0.07         0.39         4.24         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 
        0.10         0.13        79.73        37.78        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
        2.60        21.76        66.31        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
        6.02        29.16        13.64        55.69         5.62        25.81 
TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
      102.74        30.61        73.38        30.15        26.83        30.51 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-A73G 
       29.56        73.81        12.26         9.30        27.72       100.96 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
        0.53        59.18        55.40        63.48        12.00        15.42 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        13.15        48.49        40.77        38.04 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
        5.62        33.83        34.09        31.53        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR 
       28.41        25.08        20.91         3.02         3.95        57.27 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA 
        9.67         9.86         9.63         4.64        11.31        14.79 
TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       15.45        35.08        79.10        59.93        61.87        61.38 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY 
       55.86        54.05        13.41        13.35         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB 
        0.20         0.20        13.15         0.20         0.20        10.98 
TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        0.62        23.97         8.12         0.33        60.36         1.22 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 
       58.49        14.86        21.53        14.70        17.10         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5N0 
       11.80         9.70         0.89         2.14         3.02        37.71 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       17.06        11.84        13.38        24.36        12.72         5.92 
TCGA-MI-A75G TCGA-O8-A75V TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB 
       18.38         4.44        15.39        15.52        24.13        17.29 
TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
       14.40        15.98         7.04         0.99         4.01        13.55 
TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       24.43        35.05 

$`DEL PEAK  8(4Q22.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        7.10        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I 
        2.99        25.32        69.57        44.42        22.36        12.72 
TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA 
        7.46         4.80         2.86         3.39         3.32         0.07 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       83.57       113.00         0.46        51.29        90.71        79.40 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z 
       19.79        75.65         6.71        18.35        21.14        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
        0.36        33.14        32.52        30.97        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
      108.76         0.30        80.75        78.84        10.98         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD 
       10.98         1.45        13.48        11.41        65.75        12.53 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACQ TCGA-DD-AACX 
        6.41        53.19        60.10         0.30        14.33         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADF 
        4.50        18.54        21.63        22.09        30.58         3.78 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS 
       24.00        24.13         0.39        17.33         5.29         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 
        8.28         6.67         9.47         9.86         8.52        12.56 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP 
       12.69        12.16        16.37        15.65        15.65        79.07 
TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       72.26        56.48        58.78        49.48        47.70        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J 
       15.85        13.91         0.23        13.41         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        11.74         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10        27.88         6.38         0.13         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG 
        0.39        51.06        53.79        28.27        30.74        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        11.97        20.42 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 
        7.76        12.03         5.98        11.24         8.55         9.17 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 
        1.02         2.20         2.66        20.75         4.01         2.14 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        4.27         9.57        16.67        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       58.88        16.37        21.01         2.04        21.04        19.04 
TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CV 
       14.96         1.71         8.32         4.57         1.02         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57         0.69        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                       102.74                        113.00 
  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE 
                        14.50                         14.68 
[1] "0.1 - 102.7 (14.5)" "0.0 - 113.0 (14.7)"
[1] "hr=" "1.1"
D37V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  8(4Q22.3) MUTATED        69       37         2         25
  DEL PEAK  8(4Q22.3) WILD-TYPE      77       35         0         27
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  8(4Q22.3) MUTATED            3          2        2         1
  DEL PEAK  8(4Q22.3) WILD-TYPE          4          5        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK  8(4Q22.3) MUTATED           1
  DEL PEAK  8(4Q22.3) WILD-TYPE         1
D37V3, multiclass
            clus
vv           DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  STAGE I                             69                            77
  STAGE II                            37                            35
  STAGE III                            2                             0
  STAGE IIIA                          25                            27
  STAGE IIIB                           3                             4
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            1                             0
  STAGE IVB                            1                             1
[1] 9 2
[1] 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(4Q22.3) MUTATED      71 40 32  5
  DEL PEAK  8(4Q22.3) WILD-TYPE    84 38 32  7
D37V4, multiclass
       clus
vv      DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  T0+T1                          71                            84
  T2                             40                            38
  T3                             32                            32
  T4                              5                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED   110   2
  DEL PEAK  8(4Q22.3) WILD-TYPE 112   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED    110    2
  DEL PEAK  8(4Q22.3) WILD-TYPE  112    1
   clus
vv  DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  0                         110                           112
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  8(4Q22.3) MUTATED   124   3  22
  DEL PEAK  8(4Q22.3) WILD-TYPE 114   1  47
D37V6, multiclass
    clus
vv   DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  M0                         124                           114
  M1                           3                             1
  MX                          22                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED    45 104
  DEL PEAK  8(4Q22.3) WILD-TYPE  55 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED     45  104
  DEL PEAK  8(4Q22.3) WILD-TYPE   55  107
        clus
vv       DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  FEMALE                          45                            55
  MALE                           104                           107
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  8(4Q22.3) MUTATED                         0
  DEL PEAK  8(4Q22.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  8(4Q22.3) MUTATED                        146
  DEL PEAK  8(4Q22.3) WILD-TYPE                      157
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  8(4Q22.3) MUTATED                                  3
  DEL PEAK  8(4Q22.3) WILD-TYPE                                3
D37V8, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q22.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 146
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  8(4Q22.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   157
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(4Q22.3) MUTATED   134   6   1   8
  DEL PEAK  8(4Q22.3) WILD-TYPE 140   8   0   8
D37V9, multiclass
    clus
vv   DEL PEAK  8(4Q22.3) MUTATED DEL PEAK  8(4Q22.3) WILD-TYPE
  R0                         134                           140
  R1                           6                             8
  R2                           1                             0
  RX                           8                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4Q22.3) MUTATED                                  0    80
  DEL PEAK  8(4Q22.3) WILD-TYPE                                1    61
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q22.3) MUTATED                           8    57
  DEL PEAK  8(4Q22.3) WILD-TYPE                         7    88
D37V10, multiclass
                                  clus
vv                                 DEL PEAK  8(4Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     80
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     57
                                  clus
vv                                 DEL PEAK  8(4Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       61
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.3) MUTATED     5 137
  DEL PEAK  8(4Q22.3) WILD-TYPE   3 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.3) MUTATED      5  137
  DEL PEAK  8(4Q22.3) WILD-TYPE    3  150
                        clus
vv                       DEL PEAK  8(4Q22.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       DEL PEAK  8(4Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           150
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  9(4Q35.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q35.1) MUTATED    91  46
  DEL PEAK  9(4Q35.1) WILD-TYPE 109  46
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                          137                           155 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           46                            46 
$`DEL PEAK  9(4Q35.1) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W 
       10.78        10.59         0.66        10.13        27.52         2.99 
TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12         5.03        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-A1HT 
       14.60        13.45         0.66         0.07         0.39         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EG 
       53.33         7.33         2.60         0.46        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
       49.15         6.02        29.16        13.64        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       25.81        70.06        30.61        30.15        26.83        30.51 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB 
       29.56        73.81         9.30         0.53        11.41        59.18 
TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       55.40        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        1.91        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       38.04         5.62        21.63        33.83        34.09        31.53 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       29.26        13.97        28.41        25.08        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY 
        0.39         3.02         3.95        57.27         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEB TCGA-DD-AAEE 
        9.86         9.63         4.64        11.31        12.16        16.37 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY 
       35.08        79.10        59.93        61.87        61.38        58.78 
TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       54.05        13.41        13.35         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ 
       13.15         0.20         0.20        10.98         0.62        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X 
       19.10         8.12         0.33        60.36         1.22        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 
       14.86        21.53        14.70        17.10         1.84        11.80 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 
        0.89         2.14         3.02        17.06        11.84        13.38 
TCGA-LG-A9QC TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7SH 
        5.92        18.38        20.71        58.88        16.37        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       15.52        24.13        17.29        14.40        15.98         7.04 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
        0.99         4.01        13.55        24.43        35.05 

$`DEL PEAK  9(4Q35.1) WILD-TYPE`
TCGA-4R-AA8I TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U 
        7.10        48.99        27.91        37.32        46.78        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A69I TCGA-BC-A8YO 
       25.32        23.34        69.57        44.42        12.72         7.46 
TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-DD-A115 TCGA-DD-A118 
        4.80         2.86         3.39         4.24        83.57       113.00 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 
       75.65         6.71        18.35        21.14        19.76         7.66 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        32.52        73.38        30.97        39.78        56.25 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        7.56        10.98         1.45        27.72       100.96        13.48 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACX TCGA-DD-AAD0 
       65.75        12.53        60.10         0.30         5.59         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADN 
       18.54        22.09        30.58         3.78        24.00        17.33 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
        5.29         7.10         8.28         9.47         9.86         8.52 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH 
       12.56        12.69        14.79        15.45        15.65        15.65 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW2 TCGA-DD-AAW3 
       79.07        72.26        56.48        55.86        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E 
       12.69        15.85        13.91         0.23         0.20        13.41 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 
       22.85        14.40        32.45        27.88         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.53        19.23        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42         7.76        12.03         5.98        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        9.70         9.17         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD 
       20.75         4.01         2.14        24.36        12.72         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF 
        9.57        16.67        12.85        10.85         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U 
        2.04        21.04        19.04        14.96         1.71         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.57         1.02         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        12.99        45.57        74.24         8.22 

  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                        79.73                        113.00 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                        13.84                         15.65 
[1] "0.1 - 79.7 (13.8)"  "0.0 - 113.0 (15.7)"
[1] "hr=" "1.4"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK  9(4Q35.1) MUTATED        67       40         1         28
  DEL PEAK  9(4Q35.1) WILD-TYPE      79       32         1         24
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  9(4Q35.1) MUTATED            2          2        2         1
  DEL PEAK  9(4Q35.1) WILD-TYPE          5          5        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK  9(4Q35.1) MUTATED           1
  DEL PEAK  9(4Q35.1) WILD-TYPE         1
D38V3, multiclass
            clus
vv           DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  STAGE I                             67                            79
  STAGE II                            40                            32
  STAGE III                            1                             1
  STAGE IIIA                          28                            24
  STAGE IIIB                           2                             5
  STAGE IIIC                           2                             5
  STAGE IV                             2                             0
  STAGE IVA                            1                             0
  STAGE IVB                            1                             1
[1] 9 2
[1] 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(4Q35.1) MUTATED      69 43 35  4
  DEL PEAK  9(4Q35.1) WILD-TYPE    86 35 29  8
D38V4, multiclass
       clus
vv      DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  T0+T1                          69                            86
  T2                             43                            35
  T3                             35                            29
  T4                              4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED   113   2
  DEL PEAK  9(4Q35.1) WILD-TYPE 109   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED    113    2
  DEL PEAK  9(4Q35.1) WILD-TYPE  109    1
   clus
vv  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  0                         113                           109
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  9(4Q35.1) MUTATED   124   3  24
  DEL PEAK  9(4Q35.1) WILD-TYPE 114   1  45
D38V6, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  M0                         124                           114
  M1                           3                             1
  MX                          24                            45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED    41 110
  DEL PEAK  9(4Q35.1) WILD-TYPE  59 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     41  110
  DEL PEAK  9(4Q35.1) WILD-TYPE   59  101
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  FEMALE                          41                            59
  MALE                           110                           101
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK  9(4Q35.1) MUTATED                         0
  DEL PEAK  9(4Q35.1) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK  9(4Q35.1) MUTATED                        148
  DEL PEAK  9(4Q35.1) WILD-TYPE                      155
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK  9(4Q35.1) MUTATED                                  3
  DEL PEAK  9(4Q35.1) WILD-TYPE                                3
D38V8, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q35.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 148
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK  9(4Q35.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   155
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4Q35.1) MUTATED   136   5   1   8
  DEL PEAK  9(4Q35.1) WILD-TYPE 138   9   0   8
D38V9, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  R0                         136                           138
  R1                           5                             9
  R2                           1                             0
  RX                           8                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4Q35.1) MUTATED                                  0    88
  DEL PEAK  9(4Q35.1) WILD-TYPE                                1    53
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q35.1) MUTATED                           9    54
  DEL PEAK  9(4Q35.1) WILD-TYPE                         6    91
D38V10, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     88
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     54
                                  clus
vv                                 DEL PEAK  9(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       53
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       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"
D38V11, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED     3 144
  DEL PEAK  9(4Q35.1) WILD-TYPE   5 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED      3  144
  DEL PEAK  9(4Q35.1) WILD-TYPE    5  143
                        clus
vv                       DEL PEAK  9(4Q35.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         144
                        clus
vv                       DEL PEAK  9(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           143
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 10(6Q27) MUTATION ANALYSIS
D39V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 10(6Q27) MUTATED    76  37
  DEL PEAK 10(6Q27) WILD-TYPE 124  55
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                        113                         179 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                         37                          55 
$`DEL PEAK 10(6Q27) MUTATED`
TCGA-4R-AA8I TCGA-BC-A10Q TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BD-A3ER 
        7.10        37.32         0.26         9.50        12.72         4.80 
TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 
        2.86         3.32         0.10         0.07         0.13        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 
       83.57       113.00         7.33         2.60        21.76        90.71 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
        6.71        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NH 
       55.69        19.76        25.81         0.36        33.14        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73E TCGA-DD-AA3A 
       30.51        39.78        29.56        80.75         1.45        13.48 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACI 
        0.53        59.18        12.53        63.48         6.41        53.19 
TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 
       13.15        40.77        38.04         4.50        33.83        31.53 
TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
        3.78        24.00        20.91        17.33         3.95         5.29 
TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE9 
       57.27         6.67         9.67         9.47         9.86        12.69 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVU 
       16.37        15.65        15.65        35.08        59.93        61.87 
TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y 
       58.78        54.05        49.48        47.70        13.41         0.23 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.41         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       18.74        11.93        22.85        32.45        19.10        27.88 
TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X 
        6.38         0.33        60.36         1.22        51.06        58.49 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-G3-AAV1 
       14.86        22.13        20.42         7.76         1.84        11.80 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-LG-A6GG TCGA-MI-A75E 
        9.17         0.89         2.14        37.71        12.72        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7SK TCGA-UB-A7MB 
       18.38        12.85        20.71        16.37        15.52        17.29 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZS-A9CE TCGA-ZS-A9CF 
       15.98         8.32         1.02        35.05        74.24 

$`DEL PEAK 10(6Q27) WILD-TYPE`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
       10.78        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       14.60         7.46        13.45         0.66         0.07         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11B 
        3.39         4.24         0.10        79.73        53.33         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       51.29        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14         5.62         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       73.38        30.97        26.83        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
       10.98        27.72       100.96        11.41        65.75        55.40 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       12.00        15.42        60.10         0.30         1.91        58.16 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       14.33        48.49         5.59         5.62        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       34.09        22.09        30.58        29.26        13.97        28.41 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU 
       25.08        24.13         0.39         3.02         7.10         8.28 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.86         9.63         8.52         4.64        12.56        11.31 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       14.79        12.16        15.45        79.07        79.10        72.26 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       61.38        56.48        55.86        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         0.20         0.20        13.15        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 
       10.98         0.62         9.96        14.40        23.97         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.13         0.03         0.39        53.79        28.27        30.74 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       11.97        17.10        12.03         5.98        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF 
        9.70         3.02         1.02         2.20         2.66        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        5.92         4.27         9.57        10.85        58.88         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
       21.01         2.04        21.04        19.04        15.39        24.13 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WQ-A9G7 
       14.96        14.40         1.71         7.04         4.57         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.01        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
        0.69        24.43        12.99        45.57         8.22 

  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                       0.07                        0.03 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                     113.00                      108.76 
  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE 
                      15.98                       13.91 
[1] "0.1 - 113.0 (16.0)" "0.0 - 108.8 (13.9)"
[1] "hr=" "1.1"
D39V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(6Q27) MUTATED        55       26         1         20          3
  DEL PEAK 10(6Q27) WILD-TYPE      91       46         1         32          4
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(6Q27) MUTATED            5        2         0         1
  DEL PEAK 10(6Q27) WILD-TYPE          2        0         1         1
D39V3, multiclass
            clus
vv           DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  STAGE I                           55                          91
  STAGE II                          26                          46
  STAGE III                          1                           1
  STAGE IIIA                        20                          32
  STAGE IIIB                         3                           4
  STAGE IIIC                         5                           2
  STAGE IV                           2                           0
  STAGE IVA                          0                           1
  STAGE IVB                          1                           1
[1] 9 2
[1] 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(6Q27) MUTATED      56 30 25  4
  DEL PEAK 10(6Q27) WILD-TYPE    99 48 39  8
D39V4, multiclass
       clus
vv      DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  T0+T1                        56                          99
  T2                           30                          48
  T3                           25                          39
  T4                            4                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED    82   2
  DEL PEAK 10(6Q27) WILD-TYPE 140   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED     82    2
  DEL PEAK 10(6Q27) WILD-TYPE  140    1
   clus
vv  DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  0                        82                         140
  1                         2                           1
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK 10(6Q27) MUTATED    94   3  20
  DEL PEAK 10(6Q27) WILD-TYPE 144   1  49
D39V6, multiclass
    clus
vv   DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  M0                        94                         144
  M1                         3                           1
  MX                        20                          49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED    40  77
  DEL PEAK 10(6Q27) WILD-TYPE  60 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED     40   77
  DEL PEAK 10(6Q27) WILD-TYPE   60  134
        clus
vv       DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  FEMALE                        40                          60
  MALE                          77                         134
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK 10(6Q27) MUTATED                         0                      114
  DEL PEAK 10(6Q27) WILD-TYPE                       2                      189
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 10(6Q27) MUTATED                                  3
  DEL PEAK 10(6Q27) WILD-TYPE                                3
D39V8, multiclass
                                  clus
vv                                 DEL PEAK 10(6Q27) MUTATED
  FIBROLAMELLAR CARCINOMA                                  0
  HEPATOCELLULAR CARCINOMA                               114
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         3
                                  clus
vv                                 DEL PEAK 10(6Q27) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    2
  HEPATOCELLULAR CARCINOMA                                 189
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
[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"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 10(6Q27) MUTATED   104   6   1   4
  DEL PEAK 10(6Q27) WILD-TYPE 170   8   0  12
D39V9, multiclass
    clus
vv   DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  R0                       104                         170
  R1                         6                           8
  R2                         1                           0
  RX                         4                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(6Q27) MUTATED                                  0    57
  DEL PEAK 10(6Q27) WILD-TYPE                                1    84
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q27) MUTATED                           4    54
  DEL PEAK 10(6Q27) WILD-TYPE                        11    91
D39V10, multiclass
                                  clus
vv                                 DEL PEAK 10(6Q27) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                   57
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   54
                                  clus
vv                                 DEL PEAK 10(6Q27) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     84
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     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"
D39V11, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q27) MUTATED     2 110
  DEL PEAK 10(6Q27) WILD-TYPE   6 177
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q27) MUTATED      2  110
  DEL PEAK 10(6Q27) WILD-TYPE    6  177
                        clus
vv                       DEL PEAK 10(6Q27) MUTATED DEL PEAK 10(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                       110                         177
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 11(8P23.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(8P23.2) MUTATED   134  63
  DEL PEAK 11(8P23.2) WILD-TYPE  66  29
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                          197                            95 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                           63                            29 
$`DEL PEAK 11(8P23.2) MUTATED`
TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       10.59        48.99        10.13        46.78        27.52        27.52 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        5.03        44.42        13.84         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       12.72        13.45         0.66         0.07         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
        4.24         3.32         0.10         0.13        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EE 
       53.33       113.00         7.33        21.76        90.71         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 
       21.14        55.69         5.62        19.76        25.81        17.59 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        33.14        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        26.83        30.51        39.78        29.56        73.81 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        10.98         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        1.45        27.72       100.96        59.18        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACP 
       63.48        15.42         6.41        60.10        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       14.33        48.49        40.77         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        33.83        34.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM 
       13.97        28.41         3.78        25.08        24.13         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AAE0 
       17.33         3.02         3.95         5.29        57.27         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
        8.52         4.64        12.56        11.31        12.69        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.45        16.37        15.65        15.65        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.26        59.93        61.87        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       49.48        47.70        13.41        13.35         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       27.88         8.12         6.38         0.03        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
        1.22        28.27        30.74        58.49        14.86        22.13 
TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.53        11.97        20.42         7.76        12.03         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.24         8.55         9.70         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 TCGA-KR-A7K2 
        1.02         2.20         2.66        37.71         4.01        11.84 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       13.38         5.92         4.27         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB 
        2.04        21.04        19.04        15.52        24.13        17.29 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98         7.04         8.32         1.02         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
        4.01        13.55         4.67        23.21        23.57        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

$`DEL PEAK 11(8P23.2) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10W 
        7.10        10.78         0.66        27.91        37.32         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BC-A8YO 
       25.32        23.34         1.12        69.57         9.50         7.46 
TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A11A 
        4.80         2.86         0.07         0.10        37.78         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        0.46        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EH TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       49.15         7.66        70.06        20.12       102.74       107.11 
TCGA-DD-A4NB TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AA3A 
       32.52        56.25       108.76        12.26         9.30        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACK 
        0.53        11.41        65.75        12.00        53.19         0.30 
TCGA-DD-AACL TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD6 TCGA-DD-AADJ TCGA-DD-AADL 
        1.91        38.04         5.59        22.09        24.00        20.91 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
        7.10         8.28         6.67         9.67         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEK TCGA-DD-AAVW TCGA-DD-AAVX TCGA-ED-A4XI 
        9.86        14.79        35.08        61.38        56.48        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E 
       15.85        13.91         0.23         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 
        0.20         0.20        10.98        32.45         0.13         0.33 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       51.06        53.79        21.53        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-K7-A5RF 
       14.70        17.10         1.84        11.80         9.17        20.75 
TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75G TCGA-RC-A7SH 
       17.06         2.14        24.36        12.72        18.38        15.39 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0V TCGA-ZP-A9CY TCGA-ZP-A9D1 
       14.96        14.40         4.57        25.71         0.69 

  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                       113.00                        108.76 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                        15.42                         13.48 
[1] "0.0 - 113.0 (15.4)" "0.1 - 108.8 (13.5)"
[1] "hr=" "1.1"
D40V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 11(8P23.2) MUTATED       101       47         0         34
  DEL PEAK 11(8P23.2) WILD-TYPE      45       25         2         18
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 11(8P23.2) MUTATED            5          4        2         1
  DEL PEAK 11(8P23.2) WILD-TYPE          2          3        0         0
                               vv
clus                            STAGE IVB
  DEL PEAK 11(8P23.2) MUTATED           2
  DEL PEAK 11(8P23.2) WILD-TYPE         0
D40V3, multiclass
            clus
vv           DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  STAGE I                            101                            45
  STAGE II                            47                            25
  STAGE III                            0                             2
  STAGE IIIA                          34                            18
  STAGE IIIB                           5                             2
  STAGE IIIC                           4                             3
  STAGE IV                             2                             0
  STAGE IVA                            1                             0
  STAGE IVB                            2                             0
[1] 9 2
[1] 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(8P23.2) MUTATED     107  52  43   6
  DEL PEAK 11(8P23.2) WILD-TYPE    48  26  21   6
D40V4, multiclass
       clus
vv      DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  T0+T1                         107                            48
  T2                             52                            26
  T3                             43                            21
  T4                              6                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED   144   3
  DEL PEAK 11(8P23.2) WILD-TYPE  78   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED    144    3
  DEL PEAK 11(8P23.2) WILD-TYPE   78    0
   clus
vv  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  0                         144                            78
  1                           3                             0
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK 11(8P23.2) MUTATED   158   4  48
  DEL PEAK 11(8P23.2) WILD-TYPE  80   0  21
D40V6, multiclass
    clus
vv   DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  M0                         158                            80
  M1                           4                             0
  MX                          48                            21
[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"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED    65 145
  DEL PEAK 11(8P23.2) WILD-TYPE  35  66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED     65  145
  DEL PEAK 11(8P23.2) WILD-TYPE   35   66
        clus
vv       DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  FEMALE                          65                            35
  MALE                           145                            66
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 11(8P23.2) MUTATED                         1
  DEL PEAK 11(8P23.2) WILD-TYPE                       1
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 11(8P23.2) MUTATED                        207
  DEL PEAK 11(8P23.2) WILD-TYPE                       96
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 11(8P23.2) MUTATED                                  2
  DEL PEAK 11(8P23.2) WILD-TYPE                                4
D40V8, multiclass
                                  clus
vv                                 DEL PEAK 11(8P23.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 207
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK 11(8P23.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                    96
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(8P23.2) MUTATED   183   9   1  11
  DEL PEAK 11(8P23.2) WILD-TYPE  91   5   0   5
D40V9, multiclass
    clus
vv   DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE
  R0                         183                            91
  R1                           9                             5
  R2                           1                             0
  RX                          11                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(8P23.2) MUTATED                                  1    92
  DEL PEAK 11(8P23.2) WILD-TYPE                                0    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(8P23.2) MUTATED                          11   100
  DEL PEAK 11(8P23.2) WILD-TYPE                         4    45
D40V10, multiclass
                                  clus
vv                                 DEL PEAK 11(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     92
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    100
                                  clus
vv                                 DEL PEAK 11(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       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"
D40V11, binary
                               cls
clus                              0   1
  DEL PEAK 11(8P23.2) MUTATED     6 192
  DEL PEAK 11(8P23.2) WILD-TYPE   2  95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8P23.2) MUTATED      6  192
  DEL PEAK 11(8P23.2) WILD-TYPE    2   95
                        clus
vv                       DEL PEAK 11(8P23.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         192
                        clus
vv                       DEL PEAK 11(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            95
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 12(8P12) MUTATION ANALYSIS
D41V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(8P12) MUTATED   134  59
  DEL PEAK 12(8P12) WILD-TYPE  66  33
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                        193                          99 
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                         59                          33 
$`DEL PEAK 12(8P12) MUTATED`
TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       10.59        48.99        37.32        10.13        46.78        27.52 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        5.03        44.42        13.84         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       12.72        13.45         0.66         0.07         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 
        4.24         3.32         0.10         0.07        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EE 
       53.33       113.00         7.33        21.76        90.71         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 
       21.14         5.62        19.76        17.59       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NJ 
        0.36        30.61        33.14        73.38        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       39.78        29.56        73.81         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
      100.96         0.53        59.18        55.40        12.53        63.48 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       15.42         6.41        60.10        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       48.49         5.62         4.50        18.54        21.63        33.83 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       34.09        31.53        30.58        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
        3.78        25.08        24.13        17.33         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AAE0 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
        5.29        57.27         9.86         8.52        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       12.69        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        79.10        72.26        59.93        61.87        61.38 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        13.41 
TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 
       12.69        13.35         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V 
        6.38         0.03        60.36         0.39         1.22        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A6UC 
       30.74        58.49        22.13        19.53        20.42         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       12.03         5.98         1.84        11.24         8.55         9.70 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K2 
        0.89         2.14         3.02         2.66         4.01        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       13.38        24.36         5.92         4.27         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       12.85        20.71        10.85        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        2.04        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       14.96        17.29         1.71        15.98         7.04         8.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CZ 
        1.02         0.99         4.01        13.55         4.67        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

$`DEL PEAK 12(8P12) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10U TCGA-BC-A10W 
        7.10        10.78         0.66        27.91        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A5W4 TCGA-BC-A8YO 
       25.32        23.34         1.12        69.57         9.50         7.46 
TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A11A 
        4.80         2.86         0.10         0.13        37.78         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        0.46        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 
       49.15        55.69        25.81         7.66        70.06        20.12 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NP 
      107.11        32.52        30.97        26.83        56.25       108.76 
TCGA-DD-A4NQ TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACF TCGA-DD-AACI 
       12.26        13.48        11.41        65.75        12.00        53.19 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD6 
        0.30         1.91        40.77        38.04         5.59        22.09 
TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       24.00        20.91         0.39         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAEA 
        9.67         9.63         9.47         9.86         4.64        14.79 
TCGA-DD-AAEK TCGA-DD-AAVX TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       35.08        56.48        15.85        13.91         0.23         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-FV-A23B 
       13.15        13.41         0.20         0.20        10.98        32.45 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A25Z 
        0.13         0.33        51.06        53.79        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM 
       25.64         5.92        19.23        14.70        11.97        17.10 
TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF 
       11.80         9.17         1.02         2.20        37.71        20.75 
TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A4U2 TCGA-UB-A7MC 
       17.06         2.14        12.72        18.38        58.88        14.40 
TCGA-UB-AA0V TCGA-ZP-A9CY TCGA-ZP-A9D1 
        4.57        25.71         0.69 

  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                       0.03                        0.10 
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                     113.00                      108.76 
  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE 
                      14.96                       13.91 
[1] "0.0 - 113.0 (15.0)" "0.1 - 108.8 (13.9)"
[1] "hr=" "1.1"
D41V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(8P12) MUTATED        97       47         1         32          6
  DEL PEAK 12(8P12) WILD-TYPE      49       25         1         20          1
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(8P12) MUTATED            4        2         1         2
  DEL PEAK 12(8P12) WILD-TYPE          3        0         0         0
D41V3, multiclass
            clus
vv           DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  STAGE I                           97                          49
  STAGE II                          47                          25
  STAGE III                          1                           1
  STAGE IIIA                        32                          20
  STAGE IIIB                         6                           1
  STAGE IIIC                         4                           3
  STAGE IV                           2                           0
  STAGE IVA                          1                           0
  STAGE IVB                          2                           0
[1] 9 2
[1] 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(8P12) MUTATED     103  52  43   6
  DEL PEAK 12(8P12) WILD-TYPE    52  26  21   6
D41V4, multiclass
       clus
vv      DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  T0+T1                       103                          52
  T2                           52                          26
  T3                           43                          21
  T4                            6                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P12) MUTATED   145   3
  DEL PEAK 12(8P12) WILD-TYPE  77   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED    145    3
  DEL PEAK 12(8P12) WILD-TYPE   77    0
   clus
vv  DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  0                       145                          77
  1                         3                           0
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK 12(8P12) MUTATED   155   4  46
  DEL PEAK 12(8P12) WILD-TYPE  83   0  23
D41V6, multiclass
    clus
vv   DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  M0                       155                          83
  M1                         4                           0
  MX                        46                          23
[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"
D41V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P12) MUTATED    64 141
  DEL PEAK 12(8P12) WILD-TYPE  36  70
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED     64  141
  DEL PEAK 12(8P12) WILD-TYPE   36   70
        clus
vv       DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  FEMALE                        64                          36
  MALE                         141                          70
[1] 2 2
[1] FALSE
                             vv
clus                          FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DEL PEAK 12(8P12) MUTATED                         1                      201
  DEL PEAK 12(8P12) WILD-TYPE                       1                      102
                             vv
clus                          HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 12(8P12) MUTATED                                  3
  DEL PEAK 12(8P12) WILD-TYPE                                3
D41V8, multiclass
                                  clus
vv                                 DEL PEAK 12(8P12) MUTATED
  FIBROLAMELLAR CARCINOMA                                  1
  HEPATOCELLULAR CARCINOMA                               201
  HEPATOCHOLANGIOCARCINOMA (MIXED)                         3
                                  clus
vv                                 DEL PEAK 12(8P12) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                    1
  HEPATOCELLULAR CARCINOMA                                 102
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
[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"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 12(8P12) MUTATED   178  10   1  10
  DEL PEAK 12(8P12) WILD-TYPE  96   4   0   6
D41V9, multiclass
    clus
vv   DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  R0                       178                          96
  R1                        10                           4
  R2                         1                           0
  RX                        10                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(8P12) MUTATED                                  1    91
  DEL PEAK 12(8P12) WILD-TYPE                                0    50
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(8P12) MUTATED                          11    96
  DEL PEAK 12(8P12) WILD-TYPE                         4    49
D41V10, multiclass
                                  clus
vv                                 DEL PEAK 12(8P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                   91
  BLACK OR AFRICAN AMERICAN                               11
  WHITE                                                   96
                                  clus
vv                                 DEL PEAK 12(8P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     50
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     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"
D41V11, binary
                             cls
clus                            0   1
  DEL PEAK 12(8P12) MUTATED     7 186
  DEL PEAK 12(8P12) WILD-TYPE   1 101
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(8P12) MUTATED      7  186
  DEL PEAK 12(8P12) WILD-TYPE    1  101
                        clus
vv                       DEL PEAK 12(8P12) MUTATED DEL PEAK 12(8P12) WILD-TYPE
  HISPANIC OR LATINO                             7                           1
  NOT HISPANIC OR LATINO                       186                         101
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 13(9P21.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(9P21.3) MUTATED    77  39
  DEL PEAK 13(9P21.3) WILD-TYPE 123  53
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          116                           176 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                           39                            53 
$`DEL PEAK 13(9P21.3) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       10.78        10.59        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H 
       46.78        27.52         5.03         0.26         9.50        14.60 
TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        0.07         4.24         3.32         0.10         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        83.57        53.33         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       21.76        12.95        45.11         6.02        29.16        13.64 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NI 
       55.69         5.62        25.81        30.61        73.38        26.83 
TCGA-DD-A4NO TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE 
       73.81        27.72        13.48        65.75        55.40        63.48 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       15.42         6.41        13.15        48.49        40.77        38.04 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADC TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        5.62        33.83        13.97        24.00        24.13        20.91 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE1 TCGA-DD-AAE3 
       17.33         3.95         5.29         7.10         9.63         9.86 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVQ 
        4.64        11.31        15.45        16.37        35.08        79.10 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 
       59.93        61.87        61.38        55.86        54.05        13.41 
TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
       12.69        13.35         0.20        13.15        13.41         0.20 
TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A23B 
        0.20        11.74        10.98         0.62        11.93        32.45 
TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25S 
       23.97        27.88         8.12         6.38        60.36         1.22 
TCGA-G3-A25T TCGA-G3-A3CJ TCGA-G3-A7M7 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV6 
       51.06        19.53         5.98        11.80         9.17         2.14 
TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I 
        3.02         2.20        13.38        24.36        18.38        20.71 
TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       16.37        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D0 
       15.98         7.04         8.32         0.99         4.01        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        0.69        24.43 

$`DEL PEAK 13(9P21.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
        7.10         0.66        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I 
        1.12        69.57        44.42        13.84        22.36        12.72 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 
        7.46        13.45         4.80         0.66         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 
        3.39         0.07        37.78       113.00        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.40        66.31        19.79        75.65         6.71        49.15 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       18.35        21.14        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       32.52        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       10.98         9.30         7.56        10.98         1.45       100.96 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI 
        0.53        11.41        59.18        12.53        12.00        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACX 
       60.10         0.30         1.91        58.16        14.33         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        34.09        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADM 
       30.58        29.26        28.41         3.78        25.08         0.39 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
        3.02        57.27         8.28         6.67         9.67         9.86 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        9.47         8.52        12.56        12.69        14.79        12.16 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY 
       15.65        15.65        79.07        72.26        56.48        58.78 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       49.48        47.70        15.85        13.91         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A3JL 
        0.20         0.20         0.20        18.74        19.99         9.96 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       22.85        14.40        19.10         0.13         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        53.79        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13        25.64         5.92        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 
       11.97        20.42        17.10         7.76        12.03         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       11.24         8.55         9.70         0.89         1.02         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        16.67        12.85 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-UB-A7MA 
       10.85        58.88         4.44        21.01         2.04        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 
       17.29        14.40         1.71         4.57         1.02        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
        4.67        25.71        23.21        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                        83.57                        113.00 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                       14.285                        14.550 
[1] "0.1 - 83.6 (14.3)"  "0.0 - 113.0 (14.6)"
[1] "hr=" "1.2"
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 13(9P21.3) MUTATED        55       30         0         26
  DEL PEAK 13(9P21.3) WILD-TYPE      91       42         2         26
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 13(9P21.3) MUTATED            1          2        1         1
  DEL PEAK 13(9P21.3) WILD-TYPE          6          5        1         0
                               vv
clus                            STAGE IVB
  DEL PEAK 13(9P21.3) MUTATED           1
  DEL PEAK 13(9P21.3) WILD-TYPE         1
D42V3, multiclass
            clus
vv           DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  STAGE I                             55                            91
  STAGE II                            30                            42
  STAGE III                            0                             2
  STAGE IIIA                          26                            26
  STAGE IIIB                           1                             6
  STAGE IIIC                           2                             5
  STAGE IV                             1                             1
  STAGE IVA                            1                             0
  STAGE IVB                            1                             1
[1] 9 2
[1] 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(9P21.3) MUTATED      59 34 31  3
  DEL PEAK 13(9P21.3) WILD-TYPE    96 44 33  9
D42V4, multiclass
       clus
vv      DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  T0+T1                          59                            96
  T2                             34                            44
  T3                             31                            33
  T4                              3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED    91   2
  DEL PEAK 13(9P21.3) WILD-TYPE 131   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED     91    2
  DEL PEAK 13(9P21.3) WILD-TYPE  131    1
   clus
vv  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  0                          91                           131
  1                           2                             1
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK 13(9P21.3) MUTATED    98   2  27
  DEL PEAK 13(9P21.3) WILD-TYPE 140   2  42
D42V6, multiclass
    clus
vv   DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  M0                          98                           140
  M1                           2                             2
  MX                          27                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED    34  93
  DEL PEAK 13(9P21.3) WILD-TYPE  66 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED     34   93
  DEL PEAK 13(9P21.3) WILD-TYPE   66  118
        clus
vv       DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  FEMALE                          34                            66
  MALE                            93                           118
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 13(9P21.3) MUTATED                         0
  DEL PEAK 13(9P21.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 13(9P21.3) MUTATED                        124
  DEL PEAK 13(9P21.3) WILD-TYPE                      179
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 13(9P21.3) MUTATED                                  3
  DEL PEAK 13(9P21.3) WILD-TYPE                                3
D42V8, multiclass
                                  clus
vv                                 DEL PEAK 13(9P21.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                 124
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 13(9P21.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   179
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(9P21.3) MUTATED   111   8   1   5
  DEL PEAK 13(9P21.3) WILD-TYPE 163   6   0  11
D42V9, multiclass
    clus
vv   DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  R0                         111                           163
  R1                           8                             6
  R2                           1                             0
  RX                           5                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(9P21.3) MUTATED                                  1    67
  DEL PEAK 13(9P21.3) WILD-TYPE                                0    74
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(9P21.3) MUTATED                           6    52
  DEL PEAK 13(9P21.3) WILD-TYPE                         9    93
D42V10, multiclass
                                  clus
vv                                 DEL PEAK 13(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     67
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     52
                                  clus
vv                                 DEL PEAK 13(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       74
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, binary
                               cls
clus                              0   1
  DEL PEAK 13(9P21.3) MUTATED     1 122
  DEL PEAK 13(9P21.3) WILD-TYPE   7 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED      1  122
  DEL PEAK 13(9P21.3) WILD-TYPE    7  165
                        clus
vv                       DEL PEAK 13(9P21.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         122
                        clus
vv                       DEL PEAK 13(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           165
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 14(9Q31.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(9Q31.3) MUTATED    61  33
  DEL PEAK 14(9Q31.3) WILD-TYPE 139  59
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                           94                           198 
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                           33                            59 
$`DEL PEAK 14(9Q31.3) MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       10.78        10.59        27.91        37.32        10.13        46.78 
TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 
       27.52         5.03        13.84         9.50        14.60         0.07 
TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        2.86         3.32         0.10         0.10         0.13        79.73 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF 
       53.33         7.33         2.60         0.46        21.76        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y 
       45.11         6.02        29.16        18.35        55.69         5.62 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO 
       30.61        33.14        26.83        30.51        29.56        73.81 
TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACP TCGA-DD-AACU 
       13.48        59.18        12.53        63.48        13.15        40.77 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        5.62        33.83        31.53        24.00        24.13        20.91 
TCGA-DD-AADO TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ 
        3.02        11.31        14.79        15.45        35.08        79.10 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X 
       61.87        61.38        55.86        54.05        13.41        13.35 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ 
        0.20         0.20        13.15         0.62        11.93        23.97 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A4ZP TCGA-G3-A25S 
       27.88         8.12         6.38         0.13        60.36         1.22 
TCGA-G3-A25T TCGA-G3-A3CH TCGA-G3-AAV1 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       51.06        25.64        11.80         3.02         1.02         2.20 
TCGA-MI-A75G TCGA-MI-A75I TCGA-PD-A5DF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       18.38        20.71        21.01        15.39        15.52        24.13 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-AB4B TCGA-ZP-A9CZ 
       17.29        15.98         7.04         8.32         4.01        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57        24.43        35.05        74.24 

$`DEL PEAK 14(9Q31.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
        7.10         0.66        48.99        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42         0.26        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5261 
       12.72         7.46        13.45         4.80         0.66         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        3.39         4.24         0.07        37.78        83.57       113.00 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 
        6.71        49.15        13.64        21.14        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78         0.36        32.52        73.38        30.97        30.15 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
       27.72       100.96         0.53        11.41        65.75        55.40 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX 
        1.91        58.16        14.33        48.49        38.04         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
        4.50        18.54        21.63        34.09        22.09        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADM 
       29.26        13.97        28.41         3.78        25.08         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       17.33         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
        6.67         9.67         9.86         9.63         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE 
        8.52         4.64        12.56        12.69        12.16        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX 
       15.65        15.65        79.07        72.26        59.93        56.48 
TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       58.78        49.48        47.70        12.69        15.85        13.91 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.23         0.20         0.20        13.41         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74        10.98         9.96 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 
       22.85        14.40        32.45        19.10         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        53.79        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       11.97        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.14         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
        4.27         9.57        16.67        12.85        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA 
       16.37         4.44         2.04        21.04        19.04        14.96 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 
       14.40         1.71         4.57         1.02         0.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
        4.67        25.71         0.69        12.99        45.57         8.22 

  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                        79.73                        113.00 
  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE 
                       15.750                        13.845 
[1] "0.1 - 79.7 (15.8)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.2"
D43V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 14(9Q31.3) MUTATED        39       27         0         16
  DEL PEAK 14(9Q31.3) WILD-TYPE     107       45         2         36
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 14(9Q31.3) MUTATED            2          4        1         1
  DEL PEAK 14(9Q31.3) WILD-TYPE          5          3        1         0
                               vv
clus                            STAGE IVB
  DEL PEAK 14(9Q31.3) MUTATED           2
  DEL PEAK 14(9Q31.3) WILD-TYPE         0
D43V3, multiclass
            clus
vv           DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  STAGE I                             39                           107
  STAGE II                            27                            45
  STAGE III                            0                             2
  STAGE IIIA                          16                            36
  STAGE IIIB                           2                             5
  STAGE IIIC                           4                             3
  STAGE IV                             1                             1
  STAGE IVA                            1                             0
  STAGE IVB                            2                             0
[1] 9 2
[1] 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(9Q31.3) MUTATED      43  32  20   6
  DEL PEAK 14(9Q31.3) WILD-TYPE   112  46  44   6
D43V4, multiclass
       clus
vv      DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  T0+T1                          43                           112
  T2                             32                            46
  T3                             20                            44
  T4                              6                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(9Q31.3) MUTATED    65   3
  DEL PEAK 14(9Q31.3) WILD-TYPE 157   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED     65    3
  DEL PEAK 14(9Q31.3) WILD-TYPE  157    0
   clus
vv  DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  0                          65                           157
  1                           3                             0
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK 14(9Q31.3) MUTATED    71   3  27
  DEL PEAK 14(9Q31.3) WILD-TYPE 167   1  42
D43V6, multiclass
    clus
vv   DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  M0                          71                           167
  M1                           3                             1
  MX                          27                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(9Q31.3) MUTATED    30  71
  DEL PEAK 14(9Q31.3) WILD-TYPE  70 140
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED     30   71
  DEL PEAK 14(9Q31.3) WILD-TYPE   70  140
        clus
vv       DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  FEMALE                          30                            70
  MALE                            71                           140
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 14(9Q31.3) MUTATED                         0
  DEL PEAK 14(9Q31.3) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 14(9Q31.3) MUTATED                         99
  DEL PEAK 14(9Q31.3) WILD-TYPE                      204
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 14(9Q31.3) MUTATED                                  2
  DEL PEAK 14(9Q31.3) WILD-TYPE                                4
D43V8, multiclass
                                  clus
vv                                 DEL PEAK 14(9Q31.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  99
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           2
                                  clus
vv                                 DEL PEAK 14(9Q31.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   204
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(9Q31.3) MUTATED    84   7   1   6
  DEL PEAK 14(9Q31.3) WILD-TYPE 190   7   0  10
D43V9, multiclass
    clus
vv   DEL PEAK 14(9Q31.3) MUTATED DEL PEAK 14(9Q31.3) WILD-TYPE
  R0                          84                           190
  R1                           7                             7
  R2                           1                             0
  RX                           6                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(9Q31.3) MUTATED                                  0    49
  DEL PEAK 14(9Q31.3) WILD-TYPE                                1    92
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9Q31.3) MUTATED                           5    47
  DEL PEAK 14(9Q31.3) WILD-TYPE                        10    98
D43V10, multiclass
                                  clus
vv                                 DEL PEAK 14(9Q31.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     49
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     47
                                  clus
vv                                 DEL PEAK 14(9Q31.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       92
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       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"
D43V11, binary
                               cls
clus                              0   1
  DEL PEAK 14(9Q31.3) MUTATED     1  99
  DEL PEAK 14(9Q31.3) WILD-TYPE   7 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9Q31.3) MUTATED      1   99
  DEL PEAK 14(9Q31.3) WILD-TYPE    7  188
                        clus
vv                       DEL PEAK 14(9Q31.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       DEL PEAK 14(9Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           188
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 15(10Q23.31) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 15(10Q23.31) MUTATED    53  27
  DEL PEAK 15(10Q23.31) WILD-TYPE 147  65
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             80                             212 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             27                              65 
$`DEL PEAK 15(10Q23.31) MUTATED`
TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A10Y 
        0.66        27.91        37.32        10.13         2.99        23.34 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3EP 
       44.42        13.84        22.36         9.50         7.46        13.45 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        0.66         2.86         4.24         3.32         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
        0.13        37.78        83.57       113.00         2.60        21.76 
TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NA TCGA-DD-A4NI 
       45.11        13.64         5.62        25.81        33.14        26.83 
TCGA-DD-A4NQ TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACQ 
       12.26        15.42         6.41        53.19        58.16        14.33 
TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       40.77         5.62         4.50        33.83        34.09        31.53 
TCGA-DD-AADA TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 
       30.58        20.91        17.33        57.27         9.67         9.47 
TCGA-DD-AAE8 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A8O6 
       11.31        13.41         0.23         0.20         0.20         0.20 
TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25T 
        0.20        23.97        19.10        27.88         0.33        51.06 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-HP-A5N0 
       53.79        58.49        11.97        11.80         0.89        37.71 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 
       17.06        11.84        13.38        58.88        21.01         2.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-WJ-A86L TCGA-YA-A8S7 
       15.52        24.13        17.29         1.71         1.02        13.55 
TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.69        35.05 

$`DEL PEAK 15(10Q23.31) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T 
        7.10        10.78        10.59        48.99        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF 
       27.52        25.32         1.12        69.57         5.03         0.26 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         4.80         0.07         0.39         3.39 
TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
        0.10        79.73        53.33         7.33         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       12.95        49.15         6.02        29.16        18.35        21.14 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      100.96        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK 
       55.40        12.53        63.48        12.00        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD1 
        1.91        13.15        48.49        38.04         5.59        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       21.63        22.09        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       25.08        24.00        24.13         0.39         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
        5.29         7.10         8.28         6.67         9.86         9.63 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
        9.86         8.52         4.64        12.56        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       12.16        15.45        16.37        15.65        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        79.10        72.26        59.93        61.87        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.15        13.41         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       32.45         8.12         6.38         0.13         0.03        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39         1.22        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.24         8.55         9.70         9.17         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 
        1.02         2.20         2.66        20.75         4.01         2.14 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V 
       18.38        12.85        20.71        10.85        16.37         4.44 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME 
       21.04        19.04        15.39        14.96        14.40        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV 
        7.04         8.32         4.57         0.99         4.01         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                         113.00                          108.76 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                         13.740                          14.745 
[1] "0.1 - 113.0 (13.7)" "0.0 - 108.8 (14.7)"
[1] "hr=" "1.3"
D44V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 15(10Q23.31) MUTATED        31       22         0         20
  DEL PEAK 15(10Q23.31) WILD-TYPE     115       50         2         32
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 15(10Q23.31) MUTATED            2          4        0         1
  DEL PEAK 15(10Q23.31) WILD-TYPE          5          3        2         0
                                 vv
clus                              STAGE IVB
  DEL PEAK 15(10Q23.31) MUTATED           0
  DEL PEAK 15(10Q23.31) WILD-TYPE         2
D44V3, multiclass
            clus
vv           DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  STAGE I                               31                             115
  STAGE II                              22                              50
  STAGE III                              0                               2
  STAGE IIIA                            20                              32
  STAGE IIIB                             2                               5
  STAGE IIIC                             4                               3
  STAGE IV                               0                               2
  STAGE IVA                              1                               0
  STAGE IVB                              0                               2
[1] 9 2
[1] 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(10Q23.31) MUTATED      33  24  21   7
  DEL PEAK 15(10Q23.31) WILD-TYPE   122  54  43   5
D44V4, multiclass
       clus
vv      DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  T0+T1                            33                             122
  T2                               24                              54
  T3                               21                              43
  T4                                7                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED    57   2
  DEL PEAK 15(10Q23.31) WILD-TYPE 165   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     57    2
  DEL PEAK 15(10Q23.31) WILD-TYPE  165    1
   clus
vv  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  0                            57                             165
  1                             2                               1
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 15(10Q23.31) MUTATED    67   0  19
  DEL PEAK 15(10Q23.31) WILD-TYPE 171   4  50
D44V6, multiclass
    clus
vv   DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  M0                            67                             171
  M1                             0                               4
  MX                            19                              50
[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"
D44V7, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED    29  57
  DEL PEAK 15(10Q23.31) WILD-TYPE  71 154
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     29   57
  DEL PEAK 15(10Q23.31) WILD-TYPE   71  154
        clus
vv       DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  FEMALE                            29                              71
  MALE                              57                             154
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 15(10Q23.31) MUTATED                         0
  DEL PEAK 15(10Q23.31) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 15(10Q23.31) MUTATED                         82
  DEL PEAK 15(10Q23.31) WILD-TYPE                      221
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 15(10Q23.31) MUTATED                                  4
  DEL PEAK 15(10Q23.31) WILD-TYPE                                2
D44V8, multiclass
                                  clus
vv                                 DEL PEAK 15(10Q23.31) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    82
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
                                  clus
vv                                 DEL PEAK 15(10Q23.31) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     221
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               2
[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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 15(10Q23.31) MUTATED    72   4   0   8
  DEL PEAK 15(10Q23.31) WILD-TYPE 202  10   1   8
D44V9, multiclass
    clus
vv   DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  R0                            72                             202
  R1                             4                              10
  R2                             0                               1
  RX                             8                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(10Q23.31) MUTATED                                  0    42
  DEL PEAK 15(10Q23.31) WILD-TYPE                                1    99
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(10Q23.31) MUTATED                           9    34
  DEL PEAK 15(10Q23.31) WILD-TYPE                         6   111
D44V10, multiclass
                                  clus
vv                                 DEL PEAK 15(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       42
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       34
                                  clus
vv                                 DEL PEAK 15(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         99
  BLACK OR AFRICAN AMERICAN                                      6
  WHITE                                                        111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED     2  78
  DEL PEAK 15(10Q23.31) WILD-TYPE   6 209
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED      2   78
  DEL PEAK 15(10Q23.31) WILD-TYPE    6  209
                        clus
vv                       DEL PEAK 15(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            78
                        clus
vv                       DEL PEAK 15(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             209
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 16(10Q26.13) MUTATION ANALYSIS
D45V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 16(10Q26.13) MUTATED    55  27
  DEL PEAK 16(10Q26.13) WILD-TYPE 145  65
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                             82                             210 
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                             27                              65 
$`DEL PEAK 16(10Q26.13) MUTATED`
TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A10Y 
        0.66        27.91        37.32        10.13         2.99        23.34 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3EP 
        5.03        13.84        22.36         9.50         7.46        13.45 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        0.66         2.86         3.32         0.10         0.07         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EG 
       37.78        83.57         2.60        21.76        66.31        45.11 
TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NQ 
       13.64         5.62        25.81        33.14        26.83        12.26 
TCGA-DD-A73F TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACU 
       27.72        15.42        53.19        58.16        14.33        40.77 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADL 
        5.62        33.83        34.09        31.53        30.58        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE8 
        0.39        17.33        57.27         9.67         9.47        11.31 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-ED-A97K 
       13.41         0.23         0.20         0.20         0.20         0.20 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U 
       23.97        19.10        27.88         0.33        51.06        53.79 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-K7-A5RG 
       58.49        14.86        11.97        11.80         0.89        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
       11.84        13.38        24.36        10.85        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0U 
        2.04        15.52        24.13        17.29         1.71         8.32 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.99        13.55         0.69        35.05 

$`DEL PEAK 16(10Q26.13) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T 
        7.10        10.78        10.59        48.99        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF 
       27.52        25.32         1.12        69.57        44.42         0.26 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 
       14.60        12.72         4.80         0.07         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        4.24         0.10        79.73        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED 
        0.46        51.29        90.71        79.40        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
        6.71        12.95        49.15         6.02        29.16        18.35 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        55.69        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        73.38        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      100.96        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ 
       55.40        12.53        63.48        12.00         6.41        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX 
        0.30         1.91        13.15        48.49        38.04         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC 
        4.50        18.54        21.63        22.09        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADO 
       28.41         3.78        25.08        24.00        24.13         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
        3.95         5.29         7.10         8.28         6.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 
        9.63         9.86         8.52         4.64        12.56        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       14.79        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       47.70        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20        13.15        13.41         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        32.45         8.12         6.38         0.13         0.03 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
       60.36         0.39         1.22        28.27        30.74        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.24         8.55         9.70         9.17         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        1.02         2.20         2.66        37.71        20.75         4.01 
TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
        2.14        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 
       18.38        12.85        20.71        16.37         4.44        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       19.04        15.39        14.96        14.40        15.98         7.04 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        4.57         1.02         4.01         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       23.57        24.43        12.99        45.57        74.24         8.22 

  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                          83.57                          113.00 
  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE 
                         13.740                          14.745 
[1] "0.1 - 83.6 (13.7)"  "0.0 - 113.0 (14.7)"
[1] "hr=" "1.4"
D45V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 16(10Q26.13) MUTATED        34       24         0         18
  DEL PEAK 16(10Q26.13) WILD-TYPE     112       48         2         34
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 16(10Q26.13) MUTATED            2          4        0         1
  DEL PEAK 16(10Q26.13) WILD-TYPE          5          3        2         0
                                 vv
clus                              STAGE IVB
  DEL PEAK 16(10Q26.13) MUTATED           0
  DEL PEAK 16(10Q26.13) WILD-TYPE         2
D45V3, multiclass
            clus
vv           DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  STAGE I                               34                             112
  STAGE II                              24                              48
  STAGE III                              0                               2
  STAGE IIIA                            18                              34
  STAGE IIIB                             2                               5
  STAGE IIIC                             4                               3
  STAGE IV                               0                               2
  STAGE IVA                              1                               0
  STAGE IVB                              0                               2
[1] 9 2
[1] 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(10Q26.13) MUTATED      36  26  21   7
  DEL PEAK 16(10Q26.13) WILD-TYPE   119  52  43   5
D45V4, multiclass
       clus
vv      DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  T0+T1                            36                             119
  T2                               26                              52
  T3                               21                              43
  T4                                7                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q26.13) MUTATED    61   2
  DEL PEAK 16(10Q26.13) WILD-TYPE 161   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED     61    2
  DEL PEAK 16(10Q26.13) WILD-TYPE  161    1
   clus
vv  DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  0                            61                             161
  1                             2                               1
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 16(10Q26.13) MUTATED    69   0  21
  DEL PEAK 16(10Q26.13) WILD-TYPE 169   4  48
D45V6, multiclass
    clus
vv   DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  M0                            69                             169
  M1                             0                               4
  MX                            21                              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q26.13) MUTATED    29  61
  DEL PEAK 16(10Q26.13) WILD-TYPE  71 150
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED     29   61
  DEL PEAK 16(10Q26.13) WILD-TYPE   71  150
        clus
vv       DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  FEMALE                            29                              71
  MALE                              61                             150
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 16(10Q26.13) MUTATED                         1
  DEL PEAK 16(10Q26.13) WILD-TYPE                       1
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 16(10Q26.13) MUTATED                         85
  DEL PEAK 16(10Q26.13) WILD-TYPE                      218
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 16(10Q26.13) MUTATED                                  4
  DEL PEAK 16(10Q26.13) WILD-TYPE                                2
D45V8, multiclass
                                  clus
vv                                 DEL PEAK 16(10Q26.13) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                    85
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             4
                                  clus
vv                                 DEL PEAK 16(10Q26.13) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        1
  HEPATOCELLULAR CARCINOMA                                     218
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               2
[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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 16(10Q26.13) MUTATED    75   5   0   8
  DEL PEAK 16(10Q26.13) WILD-TYPE 199   9   1   8
D45V9, multiclass
    clus
vv   DEL PEAK 16(10Q26.13) MUTATED DEL PEAK 16(10Q26.13) WILD-TYPE
  R0                            75                             199
  R1                             5                               9
  R2                             0                               1
  RX                             8                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(10Q26.13) MUTATED                                  0    43
  DEL PEAK 16(10Q26.13) WILD-TYPE                                1    98
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10Q26.13) MUTATED                           9    36
  DEL PEAK 16(10Q26.13) WILD-TYPE                         6   109
D45V10, multiclass
                                  clus
vv                                 DEL PEAK 16(10Q26.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       43
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       36
                                  clus
vv                                 DEL PEAK 16(10Q26.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         98
  BLACK OR AFRICAN AMERICAN                                      6
  WHITE                                                        109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, binary
                                 cls
clus                                0   1
  DEL PEAK 16(10Q26.13) MUTATED     3  80
  DEL PEAK 16(10Q26.13) WILD-TYPE   5 207
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q26.13) MUTATED      3   80
  DEL PEAK 16(10Q26.13) WILD-TYPE    5  207
                        clus
vv                       DEL PEAK 16(10Q26.13) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            80
                        clus
vv                       DEL PEAK 16(10Q26.13) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             207
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 17(11Q14.1) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(11Q14.1) MUTATED    38  16
  DEL PEAK 17(11Q14.1) WILD-TYPE 162  76
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            54                            238 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            16                             76 
$`DEL PEAK 17(11Q14.1) MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 
       10.78         0.66        27.91        37.32        46.78         5.03 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A113 
       13.84         0.26         4.24         0.10         0.13        79.73 
TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB 
        2.60        90.71        12.95        29.16        55.69        32.52 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A73B TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AAD5 
       73.38        26.83         9.30        59.18        13.15        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADY 
       22.09        31.53        28.41         3.02         3.95         9.67 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK TCGA-ED-A7PZ TCGA-ED-A7XO 
        9.86         4.64        15.45        35.08         0.20         0.20 
TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ 
        0.20         0.62        23.97        60.36         1.22        11.97 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV6 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 
       11.80         9.70         2.14        17.06        11.84        13.38 
TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 
       19.04        24.13        14.96        14.40         7.04        13.55 

$`DEL PEAK 17(11Q14.1) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        7.10        10.59        48.99        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         0.07         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.07         0.10        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
      113.00         7.33         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
        6.02        18.35        13.64        21.14         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF 
      107.11        13.78         0.36        30.61        33.14        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        7.56        10.98         1.45        27.72       100.96        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        65.75        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        33.83 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       30.58        29.26        13.97         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR 
       24.13        20.91         0.39        17.33         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        7.10         8.28         6.67         9.86         9.63         9.47 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        8.52        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        15.65        15.65        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        14.70        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 
       12.03         5.98         1.84        11.24         8.55         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       20.75         4.01         2.14        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        4.27         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       21.04        15.39        15.52        17.29         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV 
        8.32         4.57         1.02         0.99         4.01         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                         90.71                         113.00 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                        13.265                         15.125 
[1] "0.1 - 90.7 (13.3)"  "0.0 - 113.0 (15.1)"
[1] "hr=" "1.1"
D46V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 17(11Q14.1) MUTATED        26       12         0         17
  DEL PEAK 17(11Q14.1) WILD-TYPE     120       60         2         35
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 17(11Q14.1) MUTATED            0          2        1         1
  DEL PEAK 17(11Q14.1) WILD-TYPE          7          5        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 17(11Q14.1) MUTATED           0
  DEL PEAK 17(11Q14.1) WILD-TYPE         2
D46V3, multiclass
            clus
vv           DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  STAGE I                              26                            120
  STAGE II                             12                             60
  STAGE III                             0                              2
  STAGE IIIA                           17                             35
  STAGE IIIB                            0                              7
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             1                              0
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(11Q14.1) MUTATED      28  14  19   1
  DEL PEAK 17(11Q14.1) WILD-TYPE   127  64  45  11
D46V4, multiclass
       clus
vv      DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  T0+T1                           28                            127
  T2                              14                             64
  T3                              19                             45
  T4                               1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                                cls
clus                               0   1
  DEL PEAK 17(11Q14.1) MUTATED    47   2
  DEL PEAK 17(11Q14.1) WILD-TYPE 175   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED     47    2
  DEL PEAK 17(11Q14.1) WILD-TYPE  175    1
   clus
vv  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  0                           47                            175
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 17(11Q14.1) MUTATED    51   1  10
  DEL PEAK 17(11Q14.1) WILD-TYPE 187   3  59
D46V6, multiclass
    clus
vv   DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  M0                           51                            187
  M1                            1                              3
  MX                           10                             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(11Q14.1) MUTATED    20  42
  DEL PEAK 17(11Q14.1) WILD-TYPE  80 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED     20   42
  DEL PEAK 17(11Q14.1) WILD-TYPE   80  169
        clus
vv       DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  FEMALE                           20                             80
  MALE                             42                            169
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 17(11Q14.1) MUTATED                         1
  DEL PEAK 17(11Q14.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 17(11Q14.1) MUTATED                         58
  DEL PEAK 17(11Q14.1) WILD-TYPE                      245
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 17(11Q14.1) MUTATED                                  3
  DEL PEAK 17(11Q14.1) WILD-TYPE                                3
D46V8, multiclass
                                  clus
vv                                 DEL PEAK 17(11Q14.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   58
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 17(11Q14.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    245
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              3
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 17(11Q14.1) MUTATED    54   5   0   3
  DEL PEAK 17(11Q14.1) WILD-TYPE 220   9   1  13
D46V9, multiclass
    clus
vv   DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE
  R0                           54                            220
  R1                            5                              9
  R2                            0                              1
  RX                            3                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(11Q14.1) MUTATED                                  0    29
  DEL PEAK 17(11Q14.1) WILD-TYPE                                1   112
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(11Q14.1) MUTATED                           4    29
  DEL PEAK 17(11Q14.1) WILD-TYPE                        11   116
D46V10, multiclass
                                  clus
vv                                 DEL PEAK 17(11Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      29
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      29
                                  clus
vv                                 DEL PEAK 17(11Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       112
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, binary
                                cls
clus                               0   1
  DEL PEAK 17(11Q14.1) MUTATED     3  55
  DEL PEAK 17(11Q14.1) WILD-TYPE   5 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q14.1) MUTATED      3   55
  DEL PEAK 17(11Q14.1) WILD-TYPE    5  232
                        clus
vv                       DEL PEAK 17(11Q14.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       DEL PEAK 17(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            232
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 18(11Q24.2) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(11Q24.2) MUTATED    51  19
  DEL PEAK 18(11Q24.2) WILD-TYPE 149  73
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            70                            222 
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                            19                             73 
$`DEL PEAK 18(11Q24.2) MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 
       10.78         0.66        27.91        37.32        46.78         5.03 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3M9 
       13.84         0.26        14.60         0.66         4.24         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF 
        0.07         0.13        79.73         2.60        90.71        12.95 
TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NN 
       29.16        55.69        32.52        73.38        26.83        29.56 
TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AAD5 
        9.30         1.45        59.18        53.19        13.15        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADY 
       22.09        31.53        28.41         3.02         3.95         9.67 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVP 
        9.47         9.86         4.64        15.45        35.08        79.07 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A4ZP 
        0.20         0.20         0.20         0.62        23.97        60.36 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A5SJ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        1.22        53.79        11.97         8.55        11.80         9.70 
TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-PD-A5DF 
        2.14         1.02        17.06        11.84        13.38        21.01 
TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       19.04        24.13        14.96        14.40        15.98         7.04 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.01        13.55        23.21        23.57 

$`DEL PEAK 18(11Q24.2) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        7.10        10.59        48.99        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
       22.36         9.50        12.72         7.46        13.45         4.80 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MB 
        0.07         2.86         0.39         3.39         3.32         0.10 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        45.11        49.15         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.61        33.14        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G 
       78.84        10.98         7.56        10.98        27.72       100.96 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
       13.48         0.53        11.41        65.75        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        33.83 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       30.58        29.26        13.97         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR 
       24.13        20.91         0.39        17.33         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE4 
        7.10         8.28         6.67         9.86         9.63         8.52 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE 
       12.56        11.31        12.69        14.79        12.16        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       15.65        15.65        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.23         0.20         0.20        13.15        13.41         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74        10.98         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03         0.33         0.39 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.24         9.17         0.89         3.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG 
       37.71        20.75         4.01         2.14        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 
       20.71        10.85        58.88        16.37         4.44         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0U 
       21.04        15.39        15.52        17.29         1.71         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D1 
        4.57         1.02         0.99         4.67        25.71         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        35.05        74.24         8.22 

  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                         90.71                         113.00 
  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE 
                        13.465                         15.125 
[1] "0.1 - 90.7 (13.5)"  "0.0 - 113.0 (15.1)"
[1] "hr=" "1"  
D47V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 18(11Q24.2) MUTATED        33       17         0         19
  DEL PEAK 18(11Q24.2) WILD-TYPE     113       55         2         33
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 18(11Q24.2) MUTATED            1          2        1         1
  DEL PEAK 18(11Q24.2) WILD-TYPE          6          5        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 18(11Q24.2) MUTATED           0
  DEL PEAK 18(11Q24.2) WILD-TYPE         2
D47V3, multiclass
            clus
vv           DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  STAGE I                              33                            113
  STAGE II                             17                             55
  STAGE III                             0                              2
  STAGE IIIA                           19                             33
  STAGE IIIB                            1                              6
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             1                              0
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(11Q24.2) MUTATED      37  19  21   2
  DEL PEAK 18(11Q24.2) WILD-TYPE   118  59  43  10
D47V4, multiclass
       clus
vv      DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  T0+T1                           37                            118
  T2                              19                             59
  T3                              21                             43
  T4                               2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V5, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED    57   2
  DEL PEAK 18(11Q24.2) WILD-TYPE 165   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED     57    2
  DEL PEAK 18(11Q24.2) WILD-TYPE  165    1
   clus
vv  DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  0                           57                            165
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 18(11Q24.2) MUTATED    63   1  15
  DEL PEAK 18(11Q24.2) WILD-TYPE 175   3  54
D47V6, multiclass
    clus
vv   DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  M0                           63                            175
  M1                            1                              3
  MX                           15                             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED    26  53
  DEL PEAK 18(11Q24.2) WILD-TYPE  74 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED     26   53
  DEL PEAK 18(11Q24.2) WILD-TYPE   74  158
        clus
vv       DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  FEMALE                           26                             74
  MALE                             53                            158
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 18(11Q24.2) MUTATED                         1
  DEL PEAK 18(11Q24.2) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 18(11Q24.2) MUTATED                         75
  DEL PEAK 18(11Q24.2) WILD-TYPE                      228
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 18(11Q24.2) MUTATED                                  3
  DEL PEAK 18(11Q24.2) WILD-TYPE                                3
D47V8, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q24.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   75
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 18(11Q24.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    228
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              3
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 18(11Q24.2) MUTATED    68   5   0   5
  DEL PEAK 18(11Q24.2) WILD-TYPE 206   9   1  11
D47V9, multiclass
    clus
vv   DEL PEAK 18(11Q24.2) MUTATED DEL PEAK 18(11Q24.2) WILD-TYPE
  R0                           68                            206
  R1                            5                              9
  R2                            0                              1
  RX                            5                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(11Q24.2) MUTATED                                  0    38
  DEL PEAK 18(11Q24.2) WILD-TYPE                                1   103
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(11Q24.2) MUTATED                           6    35
  DEL PEAK 18(11Q24.2) WILD-TYPE                         9   110
D47V10, multiclass
                                  clus
vv                                 DEL PEAK 18(11Q24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      38
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      35
                                  clus
vv                                 DEL PEAK 18(11Q24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       103
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                                cls
clus                               0   1
  DEL PEAK 18(11Q24.2) MUTATED     3  72
  DEL PEAK 18(11Q24.2) WILD-TYPE   5 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(11Q24.2) MUTATED      3   72
  DEL PEAK 18(11Q24.2) WILD-TYPE    5  215
                        clus
vv                       DEL PEAK 18(11Q24.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           72
                        clus
vv                       DEL PEAK 18(11Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            215
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 19(12P12.1) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(12P12.1) MUTATED    38  19
  DEL PEAK 19(12P12.1) WILD-TYPE 162  73
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            57                            235 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                            19                             73 
$`DEL PEAK 19(12P12.1) MUTATED`
TCGA-BC-4073 TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BD-A3EP 
       27.91        23.34        13.84         0.26         9.50        13.45 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH 
        3.32         0.07         0.13         7.33        45.11        49.15 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 
       29.16        13.64        55.69         5.62         7.66        13.78 
TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A73F 
       33.14        30.15        26.83        30.51        73.81        27.72 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACU TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADD 
       63.48        15.42        40.77        34.09        31.53        28.41 
TCGA-DD-AADJ TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEK 
       24.00         0.39         3.02         9.86        16.37        35.08 
TCGA-DD-AAVP TCGA-DD-AAVU TCGA-ED-A7XP TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A3R2 
       79.07        61.87        13.15         0.62         8.12         6.38 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A7M6 TCGA-G3-AAV0 TCGA-G3-AAV3 
        0.33         1.22        21.53        12.03         8.55         9.17 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-PD-A5DF 
        3.02         1.02        18.38        20.71        10.85        21.01 
TCGA-RC-A7SK TCGA-UB-AA0U TCGA-ZP-A9D1 
       15.52         8.32         0.69 

$`DEL PEAK 19(12P12.1) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-A10Q 
        7.10        10.78        10.59         0.66        48.99        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        69.57         5.03        44.42        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72         7.46         4.80         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A113 
        0.39         3.39         4.24         0.10         0.10        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V 
       75.65         6.71        12.95         6.02        18.35        21.14 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
      107.11         0.36        30.61        32.52        73.38        30.97 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       59.18        55.40        12.53        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       21.63        33.83        22.09        30.58        29.26        13.97 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADP 
        3.78        25.08        24.13        20.91        17.33         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.86         9.63         9.47         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG 
       11.31        12.69        14.79        12.16        15.45        15.65 
TCGA-DD-AAEH TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       15.65        79.10        72.26        59.93        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20         0.20         0.20        13.41         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74        10.98         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       27.88         0.13         0.03        60.36         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
       53.79        28.27        30.74        58.49        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       20.42        17.10         7.76         5.98         1.84        11.24 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.80         9.70         0.89         2.14         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 
       16.67        12.85        58.88        16.37         4.44         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        19.04        15.39        24.13        14.96        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       14.40         1.71        15.98         7.04         4.57         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99         4.01        13.55         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                         79.07                         113.00 
  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE 
                         13.84                          14.60 
[1] "0.1 - 79.1 (13.8)"  "0.0 - 113.0 (14.6)"
[1] "hr=" "1.3"
D48V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 19(12P12.1) MUTATED        26       16         1         10
  DEL PEAK 19(12P12.1) WILD-TYPE     120       56         1         42
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 19(12P12.1) MUTATED            4          2        2         0
  DEL PEAK 19(12P12.1) WILD-TYPE          3          5        0         1
                                vv
clus                             STAGE IVB
  DEL PEAK 19(12P12.1) MUTATED           0
  DEL PEAK 19(12P12.1) WILD-TYPE         2
D48V3, multiclass
            clus
vv           DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  STAGE I                              26                            120
  STAGE II                             16                             56
  STAGE III                             1                              1
  STAGE IIIA                           10                             42
  STAGE IIIB                            4                              3
  STAGE IIIC                            2                              5
  STAGE IV                              2                              0
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(12P12.1) MUTATED      28  19  14   3
  DEL PEAK 19(12P12.1) WILD-TYPE   127  59  50   9
D48V4, multiclass
       clus
vv      DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  T0+T1                           28                            127
  T2                              19                             59
  T3                              14                             50
  T4                               3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V5, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED    47   2
  DEL PEAK 19(12P12.1) WILD-TYPE 175   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED     47    2
  DEL PEAK 19(12P12.1) WILD-TYPE  175    1
   clus
vv  DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  0                           47                            175
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 19(12P12.1) MUTATED    51   2  11
  DEL PEAK 19(12P12.1) WILD-TYPE 187   2  58
D48V6, multiclass
    clus
vv   DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  M0                           51                            187
  M1                            2                              2
  MX                           11                             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED    22  42
  DEL PEAK 19(12P12.1) WILD-TYPE  78 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED     22   42
  DEL PEAK 19(12P12.1) WILD-TYPE   78  169
        clus
vv       DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  FEMALE                           22                             78
  MALE                             42                            169
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 19(12P12.1) MUTATED                         1
  DEL PEAK 19(12P12.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 19(12P12.1) MUTATED                         63
  DEL PEAK 19(12P12.1) WILD-TYPE                      240
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 19(12P12.1) MUTATED                                  0
  DEL PEAK 19(12P12.1) WILD-TYPE                                6
D48V8, multiclass
                                  clus
vv                                 DEL PEAK 19(12P12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   63
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            0
                                  clus
vv                                 DEL PEAK 19(12P12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    240
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              6
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 19(12P12.1) MUTATED    54   4   1   3
  DEL PEAK 19(12P12.1) WILD-TYPE 220  10   0  13
D48V9, multiclass
    clus
vv   DEL PEAK 19(12P12.1) MUTATED DEL PEAK 19(12P12.1) WILD-TYPE
  R0                           54                            220
  R1                            4                             10
  R2                            1                              0
  RX                            3                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(12P12.1) MUTATED                                  0    30
  DEL PEAK 19(12P12.1) WILD-TYPE                                1   111
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(12P12.1) MUTATED                           4    28
  DEL PEAK 19(12P12.1) WILD-TYPE                        11   117
D48V10, multiclass
                                  clus
vv                                 DEL PEAK 19(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      30
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      28
                                  clus
vv                                 DEL PEAK 19(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       111
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, binary
                                cls
clus                               0   1
  DEL PEAK 19(12P12.1) MUTATED     2  57
  DEL PEAK 19(12P12.1) WILD-TYPE   6 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(12P12.1) MUTATED      2   57
  DEL PEAK 19(12P12.1) WILD-TYPE    6  230
                        clus
vv                       DEL PEAK 19(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK 19(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            230
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 20(12Q24.33) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(12Q24.33) MUTATED    25  17
  DEL PEAK 20(12Q24.33) WILD-TYPE 175  75
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             42                             250 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             17                              75 
$`DEL PEAK 20(12Q24.33) MUTATED`
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-5260 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC 
       13.84         9.50         2.86         3.32         0.07         0.13 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       45.11        49.15        13.64        55.69        19.76        25.81 
TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-AAC8 
      102.74        30.61        26.83        30.51        73.81         0.53 
TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACU TCGA-DD-AAD3 TCGA-DD-AAD8 
       65.75        63.48        15.42        40.77        33.83        31.53 
TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AADY TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVU 
        3.78         0.39         9.67         9.86        35.08        61.87 
TCGA-ED-A459 TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A496 
       13.41        13.41         0.20         0.62         8.12         0.33 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-MI-A75G TCGA-NI-A8LF TCGA-RC-A7SK TCGA-ZP-A9D1 
       30.74        14.86        18.38        16.37        15.52         0.69 

$`DEL PEAK 20(12Q24.33) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       37.32        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
        0.26        22.36        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.80         0.66         0.07         0.39         3.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.10        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y 
       12.95         6.02        29.16        18.35        21.14         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACB 
        1.45        27.72       100.96        13.48        11.41        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       55.40        12.53        12.00         6.41        53.19        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         1.91        58.16        13.15        14.33        48.49 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       34.09        22.09        30.58        29.26        13.97        28.41 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO 
       25.08        24.00        24.13        20.91        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.95         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.86         9.63         9.47         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        15.65        79.07        79.10        72.26        59.93 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       47.70        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
        0.20         0.20         0.20         0.20        13.15         0.20 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74        10.98         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       27.88         6.38         0.13         0.03        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Z 
        1.22        51.06        53.79        28.27        58.49        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       11.97        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        11.24         8.55        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        0.89         2.14         3.02         1.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       16.67        12.85        20.71        10.85        58.88         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
       21.01         2.04        21.04        19.04        15.39        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       14.96        17.29        14.40         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        8.32         4.57         1.02         0.99         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                           0.07                            0.03 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                         102.74                          113.00 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                         15.470                          14.365 
[1] "0.1 - 102.7 (15.5)" "0.0 - 113.0 (14.4)"
[1] "hr=" "1.3"
D49V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 20(12Q24.33) MUTATED        18       12         2          8
  DEL PEAK 20(12Q24.33) WILD-TYPE     128       60         0         44
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 20(12Q24.33) MUTATED            2          1        1         0
  DEL PEAK 20(12Q24.33) WILD-TYPE          5          6        1         1
                                 vv
clus                              STAGE IVB
  DEL PEAK 20(12Q24.33) MUTATED           1
  DEL PEAK 20(12Q24.33) WILD-TYPE         1
D49V3, multiclass
            clus
vv           DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  STAGE I                               18                             128
  STAGE II                              12                              60
  STAGE III                              2                               0
  STAGE IIIA                             8                              44
  STAGE IIIB                             2                               5
  STAGE IIIC                             1                               6
  STAGE IV                               1                               1
  STAGE IVA                              0                               1
  STAGE IVB                              1                               1
[1] 9 2
[1] 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(12Q24.33) MUTATED      19  13  11   3
  DEL PEAK 20(12Q24.33) WILD-TYPE   136  65  53   9
D49V4, multiclass
       clus
vv      DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  T0+T1                            19                             136
  T2                               13                              65
  T3                               11                              53
  T4                                3                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                                 cls
clus                                0   1
  DEL PEAK 20(12Q24.33) MUTATED    36   0
  DEL PEAK 20(12Q24.33) WILD-TYPE 186   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED     36    0
  DEL PEAK 20(12Q24.33) WILD-TYPE  186    3
   clus
vv  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  0                            36                             186
  1                             0                               3
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 20(12Q24.33) MUTATED    40   2   4
  DEL PEAK 20(12Q24.33) WILD-TYPE 198   2  65
D49V6, multiclass
    clus
vv   DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  M0                            40                             198
  M1                             2                               2
  MX                             4                              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(12Q24.33) MUTATED    18  28
  DEL PEAK 20(12Q24.33) WILD-TYPE  82 183
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED     18   28
  DEL PEAK 20(12Q24.33) WILD-TYPE   82  183
        clus
vv       DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  FEMALE                            18                              82
  MALE                              28                             183
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 20(12Q24.33) MUTATED                         0
  DEL PEAK 20(12Q24.33) WILD-TYPE                       2
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 20(12Q24.33) MUTATED                         45
  DEL PEAK 20(12Q24.33) WILD-TYPE                      258
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 20(12Q24.33) MUTATED                                  1
  DEL PEAK 20(12Q24.33) WILD-TYPE                                5
D49V8, multiclass
                                  clus
vv                                 DEL PEAK 20(12Q24.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      0
  HEPATOCELLULAR CARCINOMA                                    45
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
                                  clus
vv                                 DEL PEAK 20(12Q24.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        2
  HEPATOCELLULAR CARCINOMA                                     258
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               5
[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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 20(12Q24.33) MUTATED    42   1   0   2
  DEL PEAK 20(12Q24.33) WILD-TYPE 232  13   1  14
D49V9, multiclass
    clus
vv   DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  R0                            42                             232
  R1                             1                              13
  R2                             0                               1
  RX                             2                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(12Q24.33) MUTATED                                  0    25
  DEL PEAK 20(12Q24.33) WILD-TYPE                                1   116
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(12Q24.33) MUTATED                           2    18
  DEL PEAK 20(12Q24.33) WILD-TYPE                        13   127
D49V10, multiclass
                                  clus
vv                                 DEL PEAK 20(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       25
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                       18
                                  clus
vv                                 DEL PEAK 20(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                        116
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                        127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, binary
                                 cls
clus                                0   1
  DEL PEAK 20(12Q24.33) MUTATED     1  43
  DEL PEAK 20(12Q24.33) WILD-TYPE   7 244
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED      1   43
  DEL PEAK 20(12Q24.33) WILD-TYPE    7  244
                        clus
vv                       DEL PEAK 20(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            43
                        clus
vv                       DEL PEAK 20(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             244
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 21(13Q14.2) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(13Q14.2) MUTATED    91  46
  DEL PEAK 21(13Q14.2) WILD-TYPE 109  46
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                           137                            155 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                            46                             46 
$`DEL PEAK 21(13Q14.2) MUTATED`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
        7.10        10.78        10.59        37.32        10.13        27.52 
TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
        2.99        23.34         1.12         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5258 
       22.36         9.50        14.60         7.46         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK 
      113.00         2.60        21.76        12.95         6.02        18.35 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA 
       55.69         5.62        25.81       102.74        30.61        33.14 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.15        30.51        29.56        73.81        12.26         0.30 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACF 
        1.45        27.72       100.96        13.48         0.53        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       15.42         6.41        53.19         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AAD1 TCGA-DD-AAD8 TCGA-DD-AADC 
       14.33        48.49        40.77        18.54        31.53        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       28.41         3.78        25.08        24.13        20.91         0.39 
TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 
        3.02        57.27         6.67         9.67         9.86         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEE 
        9.86         8.52        11.31        14.79        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-ED-A459 TCGA-ED-A4XI 
       15.65        35.08        79.07        79.10        13.41        12.69 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A3RK 
        0.23         0.20         0.20         0.20        13.15        11.93 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T 
       27.88         8.12         6.38         0.03         1.22        51.06 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M6 
       58.49        14.86        25.64        14.70        17.10        12.03 
TCGA-G3-AAUZ TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RG 
       11.24         0.89         3.02         1.02         2.20        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A8LF 
       11.84        24.36        18.38        20.71        10.85        16.37 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.01        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-YA-A8S7 
       14.96        14.40         7.04         8.32         1.02        13.55 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       25.71        23.21        23.57        35.05         8.22 

$`DEL PEAK 21(13Q14.2) WILD-TYPE`
TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X 
        0.66        48.99        27.91        46.78        27.52        25.32 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A69I TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-A3MB 
       69.57        44.42        12.72        13.45         4.80         0.10 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33         0.46        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ 
       19.79        75.65         6.71        45.11        49.15        29.16 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND 
       20.12       107.11        13.78         0.36        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS 
       30.97        26.83        39.78        56.25       108.76        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-AAC9 
       78.84        10.98         9.30         7.56        10.98        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ 
       65.75        59.18        55.40        12.53        63.48        60.10 
TCGA-DD-AACK TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 
        0.30        38.04         5.59         5.62         4.50        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADJ 
       33.83        34.09        22.09        30.58        29.26        24.00 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE1 
       17.33         3.95         5.29         7.10         8.28         9.63 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAVR 
        4.64        12.56        12.69        12.16        15.65        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       54.05        49.48        47.70        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        13.41         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
       19.99        11.74        10.98         0.62         9.96        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A496 
       14.40        32.45        23.97        19.10         0.13         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
       60.36         0.39        53.79        28.27        30.74        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       22.13         5.92        19.53        19.23        11.97        20.42 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        7.76         5.98         1.84         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        9.17         2.14         2.66        37.71        20.75         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        13.38        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-UB-A7MB 
       16.67        12.85        58.88         4.44         2.04        17.29 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV 
        1.71        15.98         4.57         0.99         4.01         4.67 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        74.24 

  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                        113.00                         108.76 
  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE 
                         13.84                          16.67 
[1] "0.0 - 113.0 (13.8)" "0.1 - 108.8 (16.7)"
[1] "hr=" "1.4"
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 21(13Q14.2) MUTATED        62       43         1         26
  DEL PEAK 21(13Q14.2) WILD-TYPE      84       29         1         26
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 21(13Q14.2) MUTATED            3          4        0         0
  DEL PEAK 21(13Q14.2) WILD-TYPE          4          3        2         1
                                vv
clus                             STAGE IVB
  DEL PEAK 21(13Q14.2) MUTATED           2
  DEL PEAK 21(13Q14.2) WILD-TYPE         0
D50V3, multiclass
            clus
vv           DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  STAGE I                              62                             84
  STAGE II                             43                             29
  STAGE III                             1                              1
  STAGE IIIA                           26                             26
  STAGE IIIB                            3                              4
  STAGE IIIC                            4                              3
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             2                              0
[1] 9 2
[1] 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(13Q14.2) MUTATED      65 46 30 10
  DEL PEAK 21(13Q14.2) WILD-TYPE    90 32 34  2
D50V4, multiclass
       clus
vv      DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  T0+T1                           65                             90
  T2                              46                             32
  T3                              30                             34
  T4                              10                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED   112   1
  DEL PEAK 21(13Q14.2) WILD-TYPE 110   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED    112    1
  DEL PEAK 21(13Q14.2) WILD-TYPE  110    2
   clus
vv  DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  0                          112                            110
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 21(13Q14.2) MUTATED   117   2  32
  DEL PEAK 21(13Q14.2) WILD-TYPE 121   2  37
D50V6, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  M0                          117                            121
  M1                            2                              2
  MX                           32                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED    54  97
  DEL PEAK 21(13Q14.2) WILD-TYPE  46 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED     54   97
  DEL PEAK 21(13Q14.2) WILD-TYPE   46  114
        clus
vv       DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  FEMALE                           54                             46
  MALE                             97                            114
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 21(13Q14.2) MUTATED                         1
  DEL PEAK 21(13Q14.2) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 21(13Q14.2) MUTATED                        146
  DEL PEAK 21(13Q14.2) WILD-TYPE                      157
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 21(13Q14.2) MUTATED                                  4
  DEL PEAK 21(13Q14.2) WILD-TYPE                                2
D50V8, multiclass
                                  clus
vv                                 DEL PEAK 21(13Q14.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  146
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK 21(13Q14.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    157
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              2
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 21(13Q14.2) MUTATED   129   8   0  10
  DEL PEAK 21(13Q14.2) WILD-TYPE 145   6   1   6
D50V9, multiclass
    clus
vv   DEL PEAK 21(13Q14.2) MUTATED DEL PEAK 21(13Q14.2) WILD-TYPE
  R0                          129                            145
  R1                            8                              6
  R2                            0                              1
  RX                           10                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(13Q14.2) MUTATED                                  0    79
  DEL PEAK 21(13Q14.2) WILD-TYPE                                1    62
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(13Q14.2) MUTATED                           7    63
  DEL PEAK 21(13Q14.2) WILD-TYPE                         8    82
D50V10, multiclass
                                  clus
vv                                 DEL PEAK 21(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      79
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      63
                                  clus
vv                                 DEL PEAK 21(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        62
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                        82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, binary
                                cls
clus                               0   1
  DEL PEAK 21(13Q14.2) MUTATED     4 141
  DEL PEAK 21(13Q14.2) WILD-TYPE   4 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(13Q14.2) MUTATED      4  141
  DEL PEAK 21(13Q14.2) WILD-TYPE    4  146
                        clus
vv                       DEL PEAK 21(13Q14.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          141
                        clus
vv                       DEL PEAK 21(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            146
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 22(14Q23.3) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(14Q23.3) MUTATED    70  32
  DEL PEAK 22(14Q23.3) WILD-TYPE 130  60
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                           102                            190 
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                            32                             60 
$`DEL PEAK 22(14Q23.3) MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10Z TCGA-BC-A112 
       10.78         0.66        27.91        37.32         1.12         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 
       44.42         0.26        22.36        13.45         0.07         2.86 
TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        0.39         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG 
       83.57       113.00         2.60        21.76        90.71        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 
        6.02        29.16        13.64        55.69         5.62         7.66 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NO 
       13.78        30.61        32.52        30.15        26.83        73.81 
TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACE 
       12.26        27.72        13.48         0.53        65.75        63.48 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ 
       15.42         6.41        48.49        40.77         5.59         5.62 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL 
       34.09        22.09        29.26        28.41         3.78        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AAE0 
        0.39        17.33         3.02        57.27         6.67         9.86 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
        9.86         4.64        11.31        15.45        16.37        15.65 
TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       79.07        61.87        47.70        13.41         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KB 
       13.15        13.41         0.20         0.20        18.74        10.98 
TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH 
       11.93        27.88        60.36         1.22        58.49        25.64 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG 
       17.10         1.84        11.80         3.02         1.02        17.06 
TCGA-KR-A7K7 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       13.38        16.37        21.01        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D2 
       24.13        14.40         7.04         0.99         4.01        24.43 

$`DEL PEAK 22(14Q23.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
        7.10        10.59        48.99        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A217 
       27.52         2.99        25.32        23.34        69.57        13.84 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO 
        9.50        14.60        12.72         7.46         4.80         0.66 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A119 
        3.39         4.24         0.10        37.78        53.33         7.33 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        0.46        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z 
        6.71        12.95        49.15        18.35        21.14        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK 
        0.36        33.14        73.38        30.97        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25        29.56       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       10.98         9.30         7.56        10.98         1.45       100.96 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI 
       11.41        59.18        55.40        12.53        12.00        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 
       38.04         4.50        18.54        21.63        33.83        31.53 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADP 
       30.58        13.97        25.08        24.00        24.13         3.95 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
        5.29         7.10         8.28         9.67         9.63         9.47 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEH 
        8.52        12.56        12.69        14.79        12.16        15.65 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       35.08        79.10        72.26        59.93        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-ED-A4XI TCGA-ED-A5KG 
       58.78        55.86        54.05        49.48        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O5 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99        11.74         0.62         9.96        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        23.97        19.10         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        14.86        21.53        22.13         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 
       19.23        14.70        11.97        20.42         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        5.98        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV6 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        2.14         2.20         2.66        37.71        20.75         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        11.84        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57        16.67        18.38        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-UB-A7MA TCGA-UB-A7MB 
       58.88         4.44         2.04        21.04        14.96        17.29 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 
        1.71        15.98         8.32         4.57         1.02        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57         0.69        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                        113.00                         108.76 
  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE 
                         14.09                          14.65 
[1] "0.1 - 113.0 (14.1)" "0.0 - 108.8 (14.6)"
[1] "hr=" "1.1"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 22(14Q23.3) MUTATED        45       31         0         25
  DEL PEAK 22(14Q23.3) WILD-TYPE     101       41         2         27
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 22(14Q23.3) MUTATED            5          3        1         0
  DEL PEAK 22(14Q23.3) WILD-TYPE          2          4        1         1
                                vv
clus                             STAGE IVB
  DEL PEAK 22(14Q23.3) MUTATED           1
  DEL PEAK 22(14Q23.3) WILD-TYPE         1
D51V3, multiclass
            clus
vv           DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  STAGE I                              45                            101
  STAGE II                             31                             41
  STAGE III                             0                              2
  STAGE IIIA                           25                             27
  STAGE IIIB                            5                              2
  STAGE IIIC                            3                              4
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] 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(14Q23.3) MUTATED      46  34  30   5
  DEL PEAK 22(14Q23.3) WILD-TYPE   109  44  34   7
D51V4, multiclass
       clus
vv      DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  T0+T1                           46                            109
  T2                              34                             44
  T3                              30                             34
  T4                               5                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED    89   1
  DEL PEAK 22(14Q23.3) WILD-TYPE 133   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED     89    1
  DEL PEAK 22(14Q23.3) WILD-TYPE  133    2
   clus
vv  DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  0                           89                            133
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 22(14Q23.3) MUTATED    96   2  17
  DEL PEAK 22(14Q23.3) WILD-TYPE 142   2  52
D51V6, multiclass
    clus
vv   DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  M0                           96                            142
  M1                            2                              2
  MX                           17                             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED    34  81
  DEL PEAK 22(14Q23.3) WILD-TYPE  66 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED     34   81
  DEL PEAK 22(14Q23.3) WILD-TYPE   66  130
        clus
vv       DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  FEMALE                           34                             66
  MALE                             81                            130
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 22(14Q23.3) MUTATED                         1
  DEL PEAK 22(14Q23.3) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 22(14Q23.3) MUTATED                        110
  DEL PEAK 22(14Q23.3) WILD-TYPE                      193
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 22(14Q23.3) MUTATED                                  4
  DEL PEAK 22(14Q23.3) WILD-TYPE                                2
D51V8, multiclass
                                  clus
vv                                 DEL PEAK 22(14Q23.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  110
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK 22(14Q23.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    193
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              2
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 22(14Q23.3) MUTATED   100   4   0   8
  DEL PEAK 22(14Q23.3) WILD-TYPE 174  10   1   8
D51V9, multiclass
    clus
vv   DEL PEAK 22(14Q23.3) MUTATED DEL PEAK 22(14Q23.3) WILD-TYPE
  R0                          100                            174
  R1                            4                             10
  R2                            0                              1
  RX                            8                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(14Q23.3) MUTATED                                  0    65
  DEL PEAK 22(14Q23.3) WILD-TYPE                                1    76
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(14Q23.3) MUTATED                           6    42
  DEL PEAK 22(14Q23.3) WILD-TYPE                         9   103
D51V10, multiclass
                                  clus
vv                                 DEL PEAK 22(14Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      65
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 22(14Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        76
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       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"
D51V11, binary
                                cls
clus                               0   1
  DEL PEAK 22(14Q23.3) MUTATED     2 107
  DEL PEAK 22(14Q23.3) WILD-TYPE   6 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q23.3) MUTATED      2  107
  DEL PEAK 22(14Q23.3) WILD-TYPE    6  180
                        clus
vv                       DEL PEAK 22(14Q23.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          107
                        clus
vv                       DEL PEAK 22(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            180
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 23(14Q32.33) MUTATION ANALYSIS
D52V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 23(14Q32.33) MUTATED    75  31
  DEL PEAK 23(14Q32.33) WILD-TYPE 125  61
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                            106                             186 
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                             31                              61 
$`DEL PEAK 23(14Q32.33) MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10Z 
       10.78         0.66        37.32        10.13        27.52         1.12 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 
        5.03        13.84         0.26        22.36         0.07         2.86 
TCGA-CC-5261 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        0.39         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ 
       83.57         2.60        21.76        90.71        45.11        29.16 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 
       13.64        55.69         5.62         7.66        13.78        30.61 
TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ 
       32.52        30.15        26.83        30.51        73.81        12.26 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH 
      100.96        13.48        65.75        63.48        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 
       53.19        48.49        40.77         5.59         5.62        34.09 
TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADM 
       22.09        29.26        28.41         3.78        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE6 
       17.33         3.02        57.27         6.67         9.86         4.64 
TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVP 
       11.31        15.45        16.37        15.65        35.08        79.07 
TCGA-DD-AAVU TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XP 
       61.87        47.70        13.41         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK 
       13.41         0.20         0.20        18.74        10.98        11.93 
TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH 
       27.88         0.03        60.36         1.22        58.49        25.64 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-K7-A5RG 
       17.10         1.84        11.80         9.17         3.02        17.06 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A7SH TCGA-RC-A7SK 
       13.38        24.36        16.37         2.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MF TCGA-WJ-A86L 
       24.13        14.96        17.29        14.40         7.04         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D2 
        0.99         4.01        23.57        24.43 

$`DEL PEAK 23(14Q32.33) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
        7.10        10.59        48.99        27.91        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A5W4 
        2.99        25.32        23.34        69.57        44.42         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       14.60        12.72         7.46        13.45         4.80         0.66 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 
        3.39         4.24         0.10        37.78        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        7.33         0.46        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        12.95        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       21.14        19.76        25.81        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF 
      102.74       107.11         0.36        33.14        73.38        30.97 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
       27.72         0.53        11.41        59.18        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       12.00        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       14.33        38.04         4.50        18.54        21.63        33.83 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       31.53        30.58        13.97        25.08        24.00        24.13 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 
        3.95         5.29         7.10         8.28         9.67         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
        9.47         9.86         8.52        12.56        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       12.16        15.65        79.10        72.26        59.93        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-ED-A4XI 
       56.48        58.78        55.86        54.05        49.48        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A8O5 TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        0.20        19.99        11.74         0.62         9.96        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        23.97        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.13         0.33         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        14.86        21.53        22.13         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 
       19.23        14.70        11.97        20.42         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 
        5.98        11.24         8.55         9.70         0.89         2.14 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        1.02         2.20         2.66        37.71        20.75         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        11.84        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MD TCGA-UB-A7ME 
        4.44        21.01        21.04        19.04         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        8.32         4.57        13.55         4.67        25.71        23.21 
TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        12.99        45.57        35.05        74.24         8.22 

  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                         100.96                          113.00 
  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE 
                          14.68                           14.50 
[1] "0.0 - 101.0 (14.7)" "0.1 - 113.0 (14.5)"
[1] "hr=" "1"  
D52V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 23(14Q32.33) MUTATED        42       37         0         22
  DEL PEAK 23(14Q32.33) WILD-TYPE     104       35         2         30
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 23(14Q32.33) MUTATED            4          3        1         0
  DEL PEAK 23(14Q32.33) WILD-TYPE          3          4        1         1
                                 vv
clus                              STAGE IVB
  DEL PEAK 23(14Q32.33) MUTATED           1
  DEL PEAK 23(14Q32.33) WILD-TYPE         1
D52V3, multiclass
            clus
vv           DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  STAGE I                               42                             104
  STAGE II                              37                              35
  STAGE III                              0                               2
  STAGE IIIA                            22                              30
  STAGE IIIB                             4                               3
  STAGE IIIC                             3                               4
  STAGE IV                               1                               1
  STAGE IVA                              0                               1
  STAGE IVB                              1                               1
[1] 9 2
[1] 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(14Q32.33) MUTATED      44  40  28   5
  DEL PEAK 23(14Q32.33) WILD-TYPE   111  38  36   7
D52V4, multiclass
       clus
vv      DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  T0+T1                            44                             111
  T2                               40                              38
  T3                               28                              36
  T4                                5                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED    85   1
  DEL PEAK 23(14Q32.33) WILD-TYPE 137   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED     85    1
  DEL PEAK 23(14Q32.33) WILD-TYPE  137    2
   clus
vv  DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  0                            85                             137
  1                             1                               2
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 23(14Q32.33) MUTATED    94   2  21
  DEL PEAK 23(14Q32.33) WILD-TYPE 144   2  48
D52V6, multiclass
    clus
vv   DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  M0                            94                             144
  M1                             2                               2
  MX                            21                              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED    37  80
  DEL PEAK 23(14Q32.33) WILD-TYPE  63 131
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED     37   80
  DEL PEAK 23(14Q32.33) WILD-TYPE   63  131
        clus
vv       DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  FEMALE                            37                              63
  MALE                              80                             131
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 23(14Q32.33) MUTATED                         1
  DEL PEAK 23(14Q32.33) WILD-TYPE                       1
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 23(14Q32.33) MUTATED                        111
  DEL PEAK 23(14Q32.33) WILD-TYPE                      192
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 23(14Q32.33) MUTATED                                  5
  DEL PEAK 23(14Q32.33) WILD-TYPE                                1
D52V8, multiclass
                                  clus
vv                                 DEL PEAK 23(14Q32.33) MUTATED
  FIBROLAMELLAR CARCINOMA                                      1
  HEPATOCELLULAR CARCINOMA                                   111
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             5
                                  clus
vv                                 DEL PEAK 23(14Q32.33) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        1
  HEPATOCELLULAR CARCINOMA                                     192
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               1
[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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 23(14Q32.33) MUTATED   102   5   0   8
  DEL PEAK 23(14Q32.33) WILD-TYPE 172   9   1   8
D52V9, multiclass
    clus
vv   DEL PEAK 23(14Q32.33) MUTATED DEL PEAK 23(14Q32.33) WILD-TYPE
  R0                           102                             172
  R1                             5                               9
  R2                             0                               1
  RX                             8                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(14Q32.33) MUTATED                                  0    61
  DEL PEAK 23(14Q32.33) WILD-TYPE                                1    80
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(14Q32.33) MUTATED                           7    46
  DEL PEAK 23(14Q32.33) WILD-TYPE                         8    99
D52V10, multiclass
                                  clus
vv                                 DEL PEAK 23(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       61
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       46
                                  clus
vv                                 DEL PEAK 23(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         80
  BLACK OR AFRICAN AMERICAN                                      8
  WHITE                                                         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"
D52V11, binary
                                 cls
clus                                0   1
  DEL PEAK 23(14Q32.33) MUTATED     2 108
  DEL PEAK 23(14Q32.33) WILD-TYPE   6 179
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(14Q32.33) MUTATED      2  108
  DEL PEAK 23(14Q32.33) WILD-TYPE    6  179
                        clus
vv                       DEL PEAK 23(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           108
                        clus
vv                       DEL PEAK 23(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             179
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 24(15Q26.3) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(15Q26.3) MUTATED    37  24
  DEL PEAK 24(15Q26.3) WILD-TYPE 163  68
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            61                            231 
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                            24                             68 
$`DEL PEAK 24(15Q26.3) MUTATED`
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A5W4 TCGA-BC-A69H 
       10.59         0.66         5.03        44.42         9.50        14.60 
TCGA-CC-5258 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11C 
        0.07         0.07        79.73        37.78        83.57        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 
       90.71         6.02        29.16        13.64         5.62       102.74 
TCGA-DD-A4NA TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AACG 
       33.14        12.26         9.30        27.72         0.53        15.42 
TCGA-DD-AACH TCGA-DD-AACL TCGA-DD-AACS TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADK 
        6.41         1.91        48.49        29.26         3.78        24.13 
TCGA-DD-AAE1 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVX 
        9.63         8.52        12.56        35.08        79.10        56.48 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E TCGA-EP-A2KB TCGA-FV-A3I0 
       13.41         0.23         0.20        13.41        10.98        27.88 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A7M9 
        0.33        60.36        21.53        14.70        17.10         1.84 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-K7-A5RG 
        8.55        11.80         0.89         2.14         3.02        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-NI-A8LF TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-YA-A8S7 
       11.84        13.38        16.37        24.13         0.99        13.55 
TCGA-ZS-A9CF 
       74.24 

$`DEL PEAK 24(15Q26.3) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
        7.10        10.78        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69I 
        1.12        69.57        13.84         0.26        22.36        12.72 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 
        7.46        13.45         4.80         0.66         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.10         0.10         0.13 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.33       113.00         7.33         2.60         0.46        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       45.11        49.15        18.35        21.14        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       25.81         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        32.52        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76         0.30        80.75        78.84        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 
        7.56        10.98         1.45       100.96        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       53.19        60.10         0.30        58.16        13.15        14.33 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       40.77        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADM 
       13.97        28.41        25.08        24.00        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       17.33         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 
        8.28         6.67         9.67         9.86         9.47         9.86 
TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS 
       16.37        15.65        15.65        79.07        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.87        61.38        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       47.70        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       22.85        14.40        32.45        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        6.38         0.13         0.03         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
       53.79        28.27        30.74        58.49        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        11.97        20.42 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV2 TCGA-G3-AAV3 
        7.76        12.03         5.98        11.24         9.70         9.17 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        1.02         2.20         2.66        37.71        20.75         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        4.44        21.01         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        14.96        17.29        14.40         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-ZP-A9CV 
        7.04         8.32         4.57         1.02         4.01         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       45.57        35.05         8.22 

  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                        102.74                         113.00 
  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE 
                         13.41                          15.39 
[1] "0.1 - 102.7 (13.4)" "0.0 - 113.0 (15.4)"
[1] "hr=" "1.4"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 24(15Q26.3) MUTATED        25       24         1         14
  DEL PEAK 24(15Q26.3) WILD-TYPE     121       48         1         38
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(15Q26.3) MUTATED            1          3        0         0
  DEL PEAK 24(15Q26.3) WILD-TYPE          6          4        2         1
                                vv
clus                             STAGE IVB
  DEL PEAK 24(15Q26.3) MUTATED           0
  DEL PEAK 24(15Q26.3) WILD-TYPE         2
D53V3, multiclass
            clus
vv           DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  STAGE I                              25                            121
  STAGE II                             24                             48
  STAGE III                             1                              1
  STAGE IIIA                           14                             38
  STAGE IIIB                            1                              6
  STAGE IIIC                            3                              4
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(15Q26.3) MUTATED      26  25  18   1
  DEL PEAK 24(15Q26.3) WILD-TYPE   129  53  46  11
D53V4, multiclass
       clus
vv      DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  T0+T1                           26                            129
  T2                              25                             53
  T3                              18                             46
  T4                               1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED    50   2
  DEL PEAK 24(15Q26.3) WILD-TYPE 172   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED     50    2
  DEL PEAK 24(15Q26.3) WILD-TYPE  172    1
   clus
vv  DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  0                           50                            172
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 24(15Q26.3) MUTATED    62   0   8
  DEL PEAK 24(15Q26.3) WILD-TYPE 176   4  61
D53V6, multiclass
    clus
vv   DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  M0                           62                            176
  M1                            0                              4
  MX                            8                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED    23  47
  DEL PEAK 24(15Q26.3) WILD-TYPE  77 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED     23   47
  DEL PEAK 24(15Q26.3) WILD-TYPE   77  164
        clus
vv       DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  FEMALE                           23                             77
  MALE                             47                            164
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 24(15Q26.3) MUTATED                         0
  DEL PEAK 24(15Q26.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 24(15Q26.3) MUTATED                         67
  DEL PEAK 24(15Q26.3) WILD-TYPE                      236
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 24(15Q26.3) MUTATED                                  3
  DEL PEAK 24(15Q26.3) WILD-TYPE                                3
D53V8, multiclass
                                  clus
vv                                 DEL PEAK 24(15Q26.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   67
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 24(15Q26.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    236
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              3
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(15Q26.3) MUTATED    64   2   0   4
  DEL PEAK 24(15Q26.3) WILD-TYPE 210  12   1  12
D53V9, multiclass
    clus
vv   DEL PEAK 24(15Q26.3) MUTATED DEL PEAK 24(15Q26.3) WILD-TYPE
  R0                           64                            210
  R1                            2                             12
  R2                            0                              1
  RX                            4                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(15Q26.3) MUTATED                                  0    36
  DEL PEAK 24(15Q26.3) WILD-TYPE                                1   105
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(15Q26.3) MUTATED                           4    30
  DEL PEAK 24(15Q26.3) WILD-TYPE                        11   115
D53V10, multiclass
                                  clus
vv                                 DEL PEAK 24(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      36
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      30
                                  clus
vv                                 DEL PEAK 24(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       105
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                                cls
clus                               0   1
  DEL PEAK 24(15Q26.3) MUTATED     3  63
  DEL PEAK 24(15Q26.3) WILD-TYPE   5 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q26.3) MUTATED      3   63
  DEL PEAK 24(15Q26.3) WILD-TYPE    5  224
                        clus
vv                       DEL PEAK 24(15Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       DEL PEAK 24(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            224
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 25(16Q23.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(16Q23.1) MUTATED    93  37
  DEL PEAK 25(16Q23.1) WILD-TYPE 107  55
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                           130                            162 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                            37                             55 
$`DEL PEAK 25(16Q23.1) MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10W 
       10.78         0.66        27.91        10.13        46.78         2.99 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       23.34         1.12        44.42        13.84        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        7.46        13.45         0.66         0.07         2.86         0.39 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        4.24         0.10         0.10         0.13        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       53.33         2.60         0.46        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND 
       29.16         5.62        19.76         0.36        30.61        73.38 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       30.15        26.83        30.51        29.56        73.81        12.26 
TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
        9.30        27.72        55.40        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       53.19         1.91        58.16        13.15        14.33        48.49 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 
       40.77        38.04         5.62         4.50        18.54        33.83 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       30.58        29.26        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AAE0 
        0.39         3.02         3.95        57.27         6.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH 
        9.63         4.64        11.31        15.45        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       35.08        79.07        79.10        59.93        61.87        61.38 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y 
       55.86        54.05        13.41        15.85        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A23B 
        0.20         0.20         0.20        10.98        22.85        32.45 
TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
       23.97        27.88         6.38         1.22        53.79        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAUZ 
       14.86        21.53        25.64        14.70         1.84        11.24 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75G 
        2.14         3.02        13.38        24.36        12.72        18.38 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH 
       20.71        16.37         4.44         2.04        19.04        15.39 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L 
       24.13        14.96        17.29         7.04         8.32         1.02 
TCGA-WQ-A9G7 TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CG 
        0.99        23.21         0.69         8.22 

$`DEL PEAK 25(16Q23.1) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U 
        7.10        10.59        48.99        37.32        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I 
       25.32        69.57         5.03         0.26         9.50        12.72 
TCGA-BD-A3ER TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 
        4.80         3.39         3.32         0.07        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65         6.71        45.11        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        55.69        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.97        39.78        56.25       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G 
       78.84        10.98         7.56        10.98         1.45       100.96 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD 
       13.48         0.53        11.41        65.75        59.18        12.53 
TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACX TCGA-DD-AAD2 TCGA-DD-AAD5 
       63.48        60.10         0.30         5.59        21.63        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN 
       22.09        31.53        13.97        28.41         3.78        17.33 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE3 
        5.29         7.10         8.28         9.67         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE 
        8.52        12.56        12.69        14.79        12.16        16.37 
TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       72.26        56.48        58.78        49.48        47.70        12.69 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.91         0.20         0.20         0.20        13.15        13.41 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       11.93        14.40        19.10         8.12         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36         0.39        51.06        28.27        30.74 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       22.13         5.92        19.53        19.23        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-G3-AAV1 
       17.10         7.76        12.03         5.98         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.70         9.17         0.89         1.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO 
        5.92         4.27         9.57        16.67        12.85        10.85 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD 
       58.88        21.01        21.04        15.52        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       15.98         4.57         4.01        13.55         4.67        25.71 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57        24.43        12.99        45.57        35.05        74.24 

  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                         79.73                         113.00 
  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE 
                         14.91                          13.94 
[1] "0.1 - 79.7 (14.9)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1"  
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 25(16Q23.1) MUTATED        59       43         1         23
  DEL PEAK 25(16Q23.1) WILD-TYPE      87       29         1         29
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 25(16Q23.1) MUTATED            3          3        1         1
  DEL PEAK 25(16Q23.1) WILD-TYPE          4          4        1         0
                                vv
clus                             STAGE IVB
  DEL PEAK 25(16Q23.1) MUTATED           1
  DEL PEAK 25(16Q23.1) WILD-TYPE         1
D54V3, multiclass
            clus
vv           DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  STAGE I                              59                             87
  STAGE II                             43                             29
  STAGE III                             1                              1
  STAGE IIIA                           23                             29
  STAGE IIIB                            3                              4
  STAGE IIIC                            3                              4
  STAGE IV                              1                              1
  STAGE IVA                             1                              0
  STAGE IVB                             1                              1
[1] 9 2
[1] 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(16Q23.1) MUTATED      63 45 29  6
  DEL PEAK 25(16Q23.1) WILD-TYPE    92 33 35  6
D54V4, multiclass
       clus
vv      DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  T0+T1                           63                             92
  T2                              45                             33
  T3                              29                             35
  T4                               6                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED   108   2
  DEL PEAK 25(16Q23.1) WILD-TYPE 114   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED    108    2
  DEL PEAK 25(16Q23.1) WILD-TYPE  114    1
   clus
vv  DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  0                          108                            114
  1                            2                              1
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 25(16Q23.1) MUTATED   116   2  25
  DEL PEAK 25(16Q23.1) WILD-TYPE 122   2  44
D54V6, multiclass
    clus
vv   DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  M0                          116                            122
  M1                            2                              2
  MX                           25                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED    51  92
  DEL PEAK 25(16Q23.1) WILD-TYPE  49 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED     51   92
  DEL PEAK 25(16Q23.1) WILD-TYPE   49  119
        clus
vv       DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  FEMALE                           51                             49
  MALE                             92                            119
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 25(16Q23.1) MUTATED                         0
  DEL PEAK 25(16Q23.1) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 25(16Q23.1) MUTATED                        140
  DEL PEAK 25(16Q23.1) WILD-TYPE                      163
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 25(16Q23.1) MUTATED                                  3
  DEL PEAK 25(16Q23.1) WILD-TYPE                                3
D54V8, multiclass
                                  clus
vv                                 DEL PEAK 25(16Q23.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                  140
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            3
                                  clus
vv                                 DEL PEAK 25(16Q23.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    163
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              3
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(16Q23.1) MUTATED   126   7   0  10
  DEL PEAK 25(16Q23.1) WILD-TYPE 148   7   1   6
D54V9, multiclass
    clus
vv   DEL PEAK 25(16Q23.1) MUTATED DEL PEAK 25(16Q23.1) WILD-TYPE
  R0                          126                            148
  R1                            7                              7
  R2                            0                              1
  RX                           10                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(16Q23.1) MUTATED                                  0    82
  DEL PEAK 25(16Q23.1) WILD-TYPE                                1    59
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(16Q23.1) MUTATED                           7    50
  DEL PEAK 25(16Q23.1) WILD-TYPE                         8    95
D54V10, multiclass
                                  clus
vv                                 DEL PEAK 25(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      82
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      50
                                  clus
vv                                 DEL PEAK 25(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        59
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                        95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, binary
                                cls
clus                               0   1
  DEL PEAK 25(16Q23.1) MUTATED     6 132
  DEL PEAK 25(16Q23.1) WILD-TYPE   2 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q23.1) MUTATED      6  132
  DEL PEAK 25(16Q23.1) WILD-TYPE    2  155
                        clus
vv                       DEL PEAK 25(16Q23.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          132
                        clus
vv                       DEL PEAK 25(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            155
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 26(17P13.1) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(17P13.1) MUTATED   115  61
  DEL PEAK 26(17P13.1) WILD-TYPE  85  31
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                           176                            116 
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                            61                             31 
$`DEL PEAK 26(17P13.1) MUTATED`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T 
        7.10         0.66        48.99        27.91        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       27.52        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO 
       13.84         0.26        22.36         9.50        14.60         7.46 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         0.66         0.07         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        4.24         3.32         0.07         0.10         0.13        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         2.60        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       51.29        79.40        66.31        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A3 
       29.16        18.35        13.64         5.62        25.81        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74        13.78        30.61        33.14        32.52 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73A 
       30.15        26.83        30.51        73.81        12.26        10.98 
TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
        9.30         1.45        11.41        65.75        59.18        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL 
       63.48        12.00        15.42         6.41        60.10         1.91 
TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ 
       58.16        14.33        48.49        40.77         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        33.83        34.09        22.09        31.53 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADN 
       29.26        13.97        28.41         3.78        20.91        17.33 
TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       57.27         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
        8.52         4.64        11.31        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU 
       16.37        35.08        79.07        79.10        72.26        61.87 
TCGA-DD-AAVW TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       61.38        13.41         0.20         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B 
       13.41         0.20         0.20         0.62        22.85        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 
       23.97        19.10        27.88         8.12         6.38         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.33        60.36         1.22        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
       14.86        21.53        25.64        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 
       17.10        12.03         1.84        11.24        11.80         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-KR-A7K0 TCGA-KR-A7K2 
        3.02         1.02         2.20        37.71         2.14        11.84 
TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
       12.72        16.67        18.38        20.71        58.88        16.37 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        4.44        21.01         2.04        15.39        15.52        24.13 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
        1.02         4.01        13.55         0.69        24.43        12.99 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.05        74.24 

$`DEL PEAK 26(17P13.1) WILD-TYPE`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X 
       10.78        10.59        37.32        46.78         2.99        25.32 
TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A11B TCGA-DD-A1E9 
       12.72         4.80         0.10        79.73         0.46        90.71 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X 
       19.79        75.65         6.71        12.95        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4ND 
       19.76         7.66        70.06       107.11         0.36        73.38 
TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR 
       30.97        39.78        56.25        29.56       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G 
       80.75        78.84         7.56        10.98        27.72       100.96 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACP 
       13.48         0.53        12.53        53.19         0.30        13.15 
TCGA-DD-AACW TCGA-DD-AAD2 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       38.04        21.63        30.58        25.08        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
        0.39         3.02         3.95         5.29         7.10         8.28 
TCGA-DD-AAE3 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVS 
        9.86        12.56        12.69        15.65        15.65        59.93 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74        10.98         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X 
       11.93        14.40         0.13         0.39        51.06        58.49 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A6UC TCGA-G3-A7M7 
       22.13         5.92        19.53        19.23         7.76         5.98 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-K7-A5RF 
        8.55         9.70         9.17         2.14         2.66        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06         4.01        13.38        24.36         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75H TCGA-MR-A8JO TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA 
        9.57        12.85        10.85        21.04        19.04        14.96 
TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.57         0.99         4.67        25.71        23.21        23.57 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57         8.22 

  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                        113.00                         108.76 
  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE 
                        14.745                         13.695 
[1] "0.0 - 113.0 (14.7)" "0.1 - 108.8 (13.7)"
[1] "hr=" "1.4"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 26(17P13.1) MUTATED        79       47         2         34
  DEL PEAK 26(17P13.1) WILD-TYPE      67       25         0         18
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 26(17P13.1) MUTATED            6          7        2         1
  DEL PEAK 26(17P13.1) WILD-TYPE          1          0        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK 26(17P13.1) MUTATED           2
  DEL PEAK 26(17P13.1) WILD-TYPE         0
D55V3, multiclass
            clus
vv           DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  STAGE I                              79                             67
  STAGE II                             47                             25
  STAGE III                             2                              0
  STAGE IIIA                           34                             18
  STAGE IIIB                            6                              1
  STAGE IIIC                            7                              0
  STAGE IV                              2                              0
  STAGE IVA                             1                              0
  STAGE IVB                             2                              0
[1] 9 2
[1] 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(17P13.1) MUTATED      84 52 43 11
  DEL PEAK 26(17P13.1) WILD-TYPE    71 26 21  1
D55V4, multiclass
       clus
vv      DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  T0+T1                           84                             71
  T2                              52                             26
  T3                              43                             21
  T4                              11                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V5, binary
                                cls
clus                               0   1
  DEL PEAK 26(17P13.1) MUTATED   135   3
  DEL PEAK 26(17P13.1) WILD-TYPE  87   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED    135    3
  DEL PEAK 26(17P13.1) WILD-TYPE   87    0
   clus
vv  DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  0                          135                             87
  1                            3                              0
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 26(17P13.1) MUTATED   147   4  40
  DEL PEAK 26(17P13.1) WILD-TYPE  91   0  29
D55V6, multiclass
    clus
vv   DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  M0                          147                             91
  M1                            4                              0
  MX                           40                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(17P13.1) MUTATED    59 132
  DEL PEAK 26(17P13.1) WILD-TYPE  41  79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED     59  132
  DEL PEAK 26(17P13.1) WILD-TYPE   41   79
        clus
vv       DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  FEMALE                           59                             41
  MALE                            132                             79
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 26(17P13.1) MUTATED                         1
  DEL PEAK 26(17P13.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 26(17P13.1) MUTATED                        186
  DEL PEAK 26(17P13.1) WILD-TYPE                      117
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 26(17P13.1) MUTATED                                  4
  DEL PEAK 26(17P13.1) WILD-TYPE                                2
D55V8, multiclass
                                  clus
vv                                 DEL PEAK 26(17P13.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  186
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK 26(17P13.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    117
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              2
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(17P13.1) MUTATED   165  10   1  12
  DEL PEAK 26(17P13.1) WILD-TYPE 109   4   0   4
D55V9, multiclass
    clus
vv   DEL PEAK 26(17P13.1) MUTATED DEL PEAK 26(17P13.1) WILD-TYPE
  R0                          165                            109
  R1                           10                              4
  R2                            1                              0
  RX                           12                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(17P13.1) MUTATED                                  0    94
  DEL PEAK 26(17P13.1) WILD-TYPE                                1    47
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(17P13.1) MUTATED                          11    81
  DEL PEAK 26(17P13.1) WILD-TYPE                         4    64
D55V10, multiclass
                                  clus
vv                                 DEL PEAK 26(17P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      94
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      81
                                  clus
vv                                 DEL PEAK 26(17P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        47
  BLACK OR AFRICAN AMERICAN                                     4
  WHITE                                                        64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, binary
                                cls
clus                               0   1
  DEL PEAK 26(17P13.1) MUTATED     7 175
  DEL PEAK 26(17P13.1) WILD-TYPE   1 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(17P13.1) MUTATED      7  175
  DEL PEAK 26(17P13.1) WILD-TYPE    1  112
                        clus
vv                       DEL PEAK 26(17P13.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          175
                        clus
vv                       DEL PEAK 26(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            112
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 27(17P11.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(17P11.2) MUTATED    94  55
  DEL PEAK 27(17P11.2) WILD-TYPE 106  37
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           149                            143 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                            55                             37 
$`DEL PEAK 27(17P11.2) MUTATED`
TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        0.66        48.99        27.91        10.13        27.52        27.52 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36         9.50        14.60         7.46        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        0.07         0.39         3.39         4.24         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EG 
        7.33        21.76        51.29        79.40        66.31        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A3 
        6.02        29.16        18.35        13.64         5.62        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH 
       20.12       102.74        13.78        33.14        32.52        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73E 
       26.83        30.51        73.81        12.26         9.30         1.45 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH 
       11.41        65.75        55.40        63.48        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       60.10         1.91        58.16         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       18.54        33.83        34.09        22.09        31.53        29.26 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO 
       13.97         3.78        24.00        20.91        17.33         3.02 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAEA 
        6.67         9.67         9.86         9.47         8.52        14.79 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       12.16        16.37        35.08        79.07        79.10        72.26 
TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K 
       61.87        13.41         0.20        13.41         0.20         0.20 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
        0.62        22.85        32.45        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U 
        8.12         6.38         0.03        60.36         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 
       20.42        17.10        12.03         1.84        11.24        11.80 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG 
        1.02         2.20        37.71         2.14        11.84        12.72 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF 
       16.67        18.38        20.71        58.88        16.37        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
        2.04        15.52        24.13        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 
       15.98         7.04         8.32         1.02         4.01        13.55 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        35.05        74.24 

$`DEL PEAK 27(17P11.2) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10W 
        7.10        10.78        10.59        37.32        46.78         2.99 
TCGA-BC-A10X TCGA-BC-A216 TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-A3M9 
       25.32        44.42        12.72         4.80         2.86         0.10 
TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED 
       79.73         2.60         0.46        90.71        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
        6.71        12.95        49.15        21.14        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 
       25.81         7.66        70.06       107.11         0.36        30.61 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       73.38        30.97        39.78        56.25        29.56       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        10.98         7.56        10.98 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACD 
       27.72       100.96        13.48         0.53        59.18        12.53 
TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       12.00        53.19         0.30        13.15        14.33        48.49 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD2 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADI 
       40.77        38.04        21.63        30.58        28.41        25.08 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       24.13         0.39         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        8.28         9.63         9.86         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVW 
       12.69        15.45        15.65        15.65        59.93        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20        13.15         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 
       11.74        10.98         9.96        11.93        14.40         0.13 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CI TCGA-G3-A3CJ 
        0.33         0.39        51.06        58.49         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAV0 
       19.23        14.70        11.97         7.76         5.98         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ 
        9.70         9.17         0.89         2.14         3.02         2.66 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       20.75        17.06         4.01        13.38        24.36         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7S9 
        4.27         9.57        12.85        10.85         4.44        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-ZP-A9CV 
       19.04        15.39        14.96         4.57         0.99         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       25.71        23.21        23.57        45.57         8.22 

  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                        113.00                         108.76 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                         15.52                          13.38 
[1] "0.0 - 113.0 (15.5)" "0.1 - 108.8 (13.4)"
[1] "hr=" "1.5"
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 27(17P11.2) MUTATED        63       40         1         32
  DEL PEAK 27(17P11.2) WILD-TYPE      83       32         1         20
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 27(17P11.2) MUTATED            6          6        2         1
  DEL PEAK 27(17P11.2) WILD-TYPE          1          1        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK 27(17P11.2) MUTATED           1
  DEL PEAK 27(17P11.2) WILD-TYPE         1
D56V3, multiclass
            clus
vv           DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  STAGE I                              63                             83
  STAGE II                             40                             32
  STAGE III                             1                              1
  STAGE IIIA                           32                             20
  STAGE IIIB                            6                              1
  STAGE IIIC                            6                              1
  STAGE IV                              2                              0
  STAGE IVA                             1                              0
  STAGE IVB                             1                              1
[1] 9 2
[1] 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(17P11.2) MUTATED      68 45 40  9
  DEL PEAK 27(17P11.2) WILD-TYPE    87 33 24  3
D56V4, multiclass
       clus
vv      DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  T0+T1                           68                             87
  T2                              45                             33
  T3                              40                             24
  T4                               9                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V5, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED   115   3
  DEL PEAK 27(17P11.2) WILD-TYPE 107   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED    115    3
  DEL PEAK 27(17P11.2) WILD-TYPE  107    0
   clus
vv  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  0                          115                            107
  1                            3                              0
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 27(17P11.2) MUTATED   123   3  37
  DEL PEAK 27(17P11.2) WILD-TYPE 115   1  32
D56V6, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  M0                          123                            115
  M1                            3                              1
  MX                           37                             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED    52 111
  DEL PEAK 27(17P11.2) WILD-TYPE  48 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED     52  111
  DEL PEAK 27(17P11.2) WILD-TYPE   48  100
        clus
vv       DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  FEMALE                           52                             48
  MALE                            111                            100
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 27(17P11.2) MUTATED                         1
  DEL PEAK 27(17P11.2) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 27(17P11.2) MUTATED                        158
  DEL PEAK 27(17P11.2) WILD-TYPE                      145
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 27(17P11.2) MUTATED                                  4
  DEL PEAK 27(17P11.2) WILD-TYPE                                2
D56V8, multiclass
                                  clus
vv                                 DEL PEAK 27(17P11.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                  158
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            4
                                  clus
vv                                 DEL PEAK 27(17P11.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    145
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              2
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(17P11.2) MUTATED   139  10   1  10
  DEL PEAK 27(17P11.2) WILD-TYPE 135   4   0   6
D56V9, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  R0                          139                            135
  R1                           10                              4
  R2                            1                              0
  RX                           10                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(17P11.2) MUTATED                                  0    76
  DEL PEAK 27(17P11.2) WILD-TYPE                                1    65
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(17P11.2) MUTATED                          10    73
  DEL PEAK 27(17P11.2) WILD-TYPE                         5    72
D56V10, multiclass
                                  clus
vv                                 DEL PEAK 27(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      76
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      73
                                  clus
vv                                 DEL PEAK 27(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        65
  BLACK OR AFRICAN AMERICAN                                     5
  WHITE                                                        72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED     6 149
  DEL PEAK 27(17P11.2) WILD-TYPE   2 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED      6  149
  DEL PEAK 27(17P11.2) WILD-TYPE    2  138
                        clus
vv                       DEL PEAK 27(17P11.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       DEL PEAK 27(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            138
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 28(18Q21.2) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(18Q21.2) MUTATED    52  22
  DEL PEAK 28(18Q21.2) WILD-TYPE 148  70
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            74                            218 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            22                             70 
$`DEL PEAK 28(18Q21.2) MUTATED`
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 
       10.59         0.66        10.13        27.52         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       13.84         0.26         0.10       113.00         2.60         0.46 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A4 
       12.95        29.16        13.64        55.69         5.62        20.12 
TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B 
       30.61        32.52        26.83        29.56        73.81         9.30 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACI 
        1.45       100.96         0.53        59.18        63.48        53.19 
TCGA-DD-AACP TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
       13.15         5.59         5.62        34.09        22.09        30.58 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE2 
       25.08        24.00         3.02         6.67         9.86         9.47 
TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVP TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7XP 
       15.65        35.08        79.07        13.41        13.35        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A496 
       13.41         0.20        22.85        27.88         6.38         0.33 
TCGA-G3-A25S TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MR-A8JO 
        1.22        11.80         2.14        13.38        18.38        10.85 
TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       16.37         2.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZS-A9CE 
       14.40         7.04        13.55        23.21        23.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

$`DEL PEAK 28(18Q21.2) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
        7.10        10.78        48.99        27.91        37.32        46.78 
TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         0.07         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.10         0.07         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D 
       37.78        83.57        53.33         7.33        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z 
       45.11        49.15         6.02        18.35        21.14        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81         7.66        70.06        17.59       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78         0.36        33.14        73.38        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.51        39.78        56.25       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       80.75        78.84        10.98         7.56        10.98        27.72 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       13.48        11.41        65.75        55.40        12.53        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42         6.41        60.10         0.30         1.91        58.16 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD1 
       14.33        48.49        40.77        38.04         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       21.63        33.83        31.53        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
        3.78        24.13        20.91         0.39        17.33         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 
        5.29        57.27         7.10         8.28         9.67         9.63 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.86         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVQ 
       14.79        12.16        15.45        16.37        15.65        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       55.86        54.05        49.48        47.70        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        11.93        14.40        32.45        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       19.10         8.12         0.13         0.03        60.36         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
        5.98         1.84        11.24         8.55         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        11.84        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-UB-A7MA 
       20.71        58.88         4.44        21.01        21.04        14.96 
TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
       17.29         1.71        15.98         8.32         4.57         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        0.99         4.01         4.67        25.71         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       12.99        45.57 

  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                        113.00                         108.76 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                        13.740                         14.745 
[1] "0.1 - 113.0 (13.7)" "0.0 - 108.8 (14.7)"
[1] "hr=" "1"  
D57V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 28(18Q21.2) MUTATED        37       20         0         13
  DEL PEAK 28(18Q21.2) WILD-TYPE     109       52         2         39
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 28(18Q21.2) MUTATED            0          2        1         0
  DEL PEAK 28(18Q21.2) WILD-TYPE          7          5        1         1
                                vv
clus                             STAGE IVB
  DEL PEAK 28(18Q21.2) MUTATED           1
  DEL PEAK 28(18Q21.2) WILD-TYPE         1
D57V3, multiclass
            clus
vv           DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  STAGE I                              37                            109
  STAGE II                             20                             52
  STAGE III                             0                              2
  STAGE IIIA                           13                             39
  STAGE IIIB                            0                              7
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] 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(18Q21.2) MUTATED      40  22  15   2
  DEL PEAK 28(18Q21.2) WILD-TYPE   115  56  49  10
D57V4, multiclass
       clus
vv      DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  T0+T1                           40                            115
  T2                              22                             56
  T3                              15                             49
  T4                               2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V5, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED    55   1
  DEL PEAK 28(18Q21.2) WILD-TYPE 167   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     55    1
  DEL PEAK 28(18Q21.2) WILD-TYPE  167    2
   clus
vv  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  0                           55                            167
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 28(18Q21.2) MUTATED    59   2  18
  DEL PEAK 28(18Q21.2) WILD-TYPE 179   2  51
D57V6, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  M0                           59                            179
  M1                            2                              2
  MX                           18                             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED    30  49
  DEL PEAK 28(18Q21.2) WILD-TYPE  70 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     30   49
  DEL PEAK 28(18Q21.2) WILD-TYPE   70  162
        clus
vv       DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  FEMALE                           30                             70
  MALE                             49                            162
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 28(18Q21.2) MUTATED                         2
  DEL PEAK 28(18Q21.2) WILD-TYPE                       0
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 28(18Q21.2) MUTATED                         75
  DEL PEAK 28(18Q21.2) WILD-TYPE                      228
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 28(18Q21.2) MUTATED                                  2
  DEL PEAK 28(18Q21.2) WILD-TYPE                                4
D57V8, multiclass
                                  clus
vv                                 DEL PEAK 28(18Q21.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                   75
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            2
                                  clus
vv                                 DEL PEAK 28(18Q21.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       0
  HEPATOCELLULAR CARCINOMA                                    228
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              4
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(18Q21.2) MUTATED    72   2   0   5
  DEL PEAK 28(18Q21.2) WILD-TYPE 202  12   1  11
D57V9, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  R0                           72                            202
  R1                            2                             12
  R2                            0                              1
  RX                            5                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(18Q21.2) MUTATED                                  0    35
  DEL PEAK 28(18Q21.2) WILD-TYPE                                1   106
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(18Q21.2) MUTATED                           5    39
  DEL PEAK 28(18Q21.2) WILD-TYPE                        10   106
D57V10, multiclass
                                  clus
vv                                 DEL PEAK 28(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      35
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      39
                                  clus
vv                                 DEL PEAK 28(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       106
  BLACK OR AFRICAN AMERICAN                                    10
  WHITE                                                       106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED     3  71
  DEL PEAK 28(18Q21.2) WILD-TYPE   5 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED      3   71
  DEL PEAK 28(18Q21.2) WILD-TYPE    5  216
                        clus
vv                       DEL PEAK 28(18Q21.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       DEL PEAK 28(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            216
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 29(19P13.3) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(19P13.3) MUTATED    45  19
  DEL PEAK 29(19P13.3) WILD-TYPE 155  73
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            64                            228 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                            19                             73 
$`DEL PEAK 29(19P13.3) MUTATED`
TCGA-4R-AA8I TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A8YO 
        7.10         2.99         5.03         0.26        14.60         7.46 
TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 
        0.07         4.24         3.32         0.13        79.73       113.00 
TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
        2.60        45.11         6.02        29.16        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73D TCGA-DD-AACB 
        5.62        30.61        30.51        12.26        10.98        59.18 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACL TCGA-DD-AACP TCGA-DD-AACQ 
       63.48        15.42         6.41         1.91        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       48.49        40.77         5.62        34.09        22.09        31.53 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AAE6 TCGA-DD-AAE8 
       29.26        13.97        28.41        20.91         4.64        11.31 
TCGA-DD-AAEG TCGA-DD-AAVR TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-ED-A7XO 
       15.65        72.26        13.41        12.69         0.20         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        0.20         0.20         8.12         0.33        60.36         1.22 
TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV7 
       58.49        25.64        17.10        12.03        11.80         3.02 
TCGA-MI-A75C TCGA-NI-A8LF TCGA-RC-A7SK TCGA-RG-A7D4 
        9.57        16.37        15.52        24.13 

$`DEL PEAK 29(19P13.3) WILD-TYPE`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
       10.78        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        46.78        27.52        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        69.57        44.42        13.84        22.36         9.50 
TCGA-BC-A69I TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 
       12.72        13.45         4.80         0.66         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 
        3.39         0.10         0.07         0.10        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       53.33         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       49.15        18.35        21.14        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       26.83        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ 
       65.75        55.40        12.53        12.00        53.19        60.10 
TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 
        0.30        58.16        38.04         5.59         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       21.63        33.83        30.58         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       24.13         0.39        17.33         3.02         3.95         5.29 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       57.27         7.10         8.28         6.67         9.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 
        9.63         9.47         9.86         8.52        12.56        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEK 
       14.79        12.16        15.45        16.37        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        79.10        59.93        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A5KG 
       58.78        55.86        54.05        49.48        47.70        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.41         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10        27.88         6.38         0.13         0.03 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       11.97        20.42         7.76         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 
        8.55         9.70         9.17         0.89         2.14         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        4.27        16.67        18.38        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       58.88         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.39        14.96        17.29        14.40         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04         8.32         4.57         1.02         0.99         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55         4.67        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        35.05        74.24         8.22 

  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                        113.00                         108.76 
  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE 
                        13.280                         15.175 
[1] "0.1 - 113.0 (13.3)" "0.0 - 108.8 (15.2)"
[1] "hr=" "1"  
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 29(19P13.3) MUTATED        30       21         0         14
  DEL PEAK 29(19P13.3) WILD-TYPE     116       51         2         38
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 29(19P13.3) MUTATED            1          3        0         0
  DEL PEAK 29(19P13.3) WILD-TYPE          6          4        2         1
                                vv
clus                             STAGE IVB
  DEL PEAK 29(19P13.3) MUTATED           1
  DEL PEAK 29(19P13.3) WILD-TYPE         1
D58V3, multiclass
            clus
vv           DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  STAGE I                              30                            116
  STAGE II                             21                             51
  STAGE III                             0                              2
  STAGE IIIA                           14                             38
  STAGE IIIB                            1                              6
  STAGE IIIC                            3                              4
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] 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(19P13.3) MUTATED      31  21  15   5
  DEL PEAK 29(19P13.3) WILD-TYPE   124  57  49   7
D58V4, multiclass
       clus
vv      DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  T0+T1                           31                            124
  T2                              21                             57
  T3                              15                             49
  T4                               5                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V5, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED    56   1
  DEL PEAK 29(19P13.3) WILD-TYPE 166   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     56    1
  DEL PEAK 29(19P13.3) WILD-TYPE  166    2
   clus
vv  DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  0                           56                            166
  1                            1                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 29(19P13.3) MUTATED    63   1   8
  DEL PEAK 29(19P13.3) WILD-TYPE 175   3  61
D58V6, multiclass
    clus
vv   DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  M0                           63                            175
  M1                            1                              3
  MX                            8                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED    20  52
  DEL PEAK 29(19P13.3) WILD-TYPE  80 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED     20   52
  DEL PEAK 29(19P13.3) WILD-TYPE   80  159
        clus
vv       DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  FEMALE                           20                             80
  MALE                             52                            159
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 29(19P13.3) MUTATED                         0
  DEL PEAK 29(19P13.3) WILD-TYPE                       2
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 29(19P13.3) MUTATED                         71
  DEL PEAK 29(19P13.3) WILD-TYPE                      232
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 29(19P13.3) MUTATED                                  1
  DEL PEAK 29(19P13.3) WILD-TYPE                                5
D58V8, multiclass
                                  clus
vv                                 DEL PEAK 29(19P13.3) MUTATED
  FIBROLAMELLAR CARCINOMA                                     0
  HEPATOCELLULAR CARCINOMA                                   71
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 29(19P13.3) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       2
  HEPATOCELLULAR CARCINOMA                                    232
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              5
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(19P13.3) MUTATED    65   3   0   3
  DEL PEAK 29(19P13.3) WILD-TYPE 209  11   1  13
D58V9, multiclass
    clus
vv   DEL PEAK 29(19P13.3) MUTATED DEL PEAK 29(19P13.3) WILD-TYPE
  R0                           65                            209
  R1                            3                             11
  R2                            0                              1
  RX                            3                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(19P13.3) MUTATED                                  0    46
  DEL PEAK 29(19P13.3) WILD-TYPE                                1    95
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(19P13.3) MUTATED                           3    23
  DEL PEAK 29(19P13.3) WILD-TYPE                        12   122
D58V10, multiclass
                                  clus
vv                                 DEL PEAK 29(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      46
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      23
                                  clus
vv                                 DEL PEAK 29(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        95
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, binary
                                cls
clus                               0   1
  DEL PEAK 29(19P13.3) MUTATED     1  70
  DEL PEAK 29(19P13.3) WILD-TYPE   7 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(19P13.3) MUTATED      1   70
  DEL PEAK 29(19P13.3) WILD-TYPE    7  217
                        clus
vv                       DEL PEAK 29(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       DEL PEAK 29(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            217
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 30(20P12.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(20P12.1) MUTATED    12   9
  DEL PEAK 30(20P12.1) WILD-TYPE 188  83
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                            21                            271 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                             9                             83 
$`DEL PEAK 30(20P12.1) MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Z TCGA-CC-A3MC TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y 
       10.78         1.12         0.13        18.35        21.14         5.62 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-AACS 
       17.59       102.74        73.81        12.26        27.72        48.49 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADJ TCGA-DD-AADM 
        5.59         5.62        34.09        30.58        24.00         0.39 
TCGA-ED-A7PX TCGA-ED-A97K TCGA-MR-A8JO 
        0.20         0.20        10.85 

$`DEL PEAK 30(20P12.1) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         0.07         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 
        4.24         3.32         0.10         0.07         0.10        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        29.16        13.64        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
        7.66        70.06        20.12       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       26.83        30.51        39.78        56.25        29.56       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       10.98         1.45       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD0 
       58.16        13.15        14.33        40.77        38.04         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       18.54        21.63        33.83        22.09        31.53        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       13.97        28.41         3.78        25.08        24.13        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       17.33         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        8.28         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.86         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       14.79        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.23         0.20         0.20         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       11.97        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        11.24         8.55        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        0.89         2.14         3.02         1.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
       16.67        18.38        12.85        20.71        58.88        16.37 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        4.44        21.01         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04         8.32         4.57         1.02         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.01        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                          0.13                           0.03 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                        102.74                         113.00 
  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE 
                         12.26                          14.60 
[1] "0.1 - 102.7 (12.3)" "0.0 - 113.0 (14.6)"
[1] "hr=" "1.5"
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 30(20P12.1) MUTATED        11        6         1          4
  DEL PEAK 30(20P12.1) WILD-TYPE     135       66         1         48
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 30(20P12.1) MUTATED            0          0        0         0
  DEL PEAK 30(20P12.1) WILD-TYPE          7          7        2         1
                                vv
clus                             STAGE IVB
  DEL PEAK 30(20P12.1) MUTATED           1
  DEL PEAK 30(20P12.1) WILD-TYPE         1
D59V3, multiclass
            clus
vv           DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  STAGE I                              11                            135
  STAGE II                              6                             66
  STAGE III                             1                              1
  STAGE IIIA                            4                             48
  STAGE IIIB                            0                              7
  STAGE IIIC                            0                              7
  STAGE IV                              0                              2
  STAGE IVA                             0                              1
  STAGE IVB                             1                              1
[1] 9 2
[1] 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(20P12.1) MUTATED      11   6   5   1
  DEL PEAK 30(20P12.1) WILD-TYPE   144  72  59  11
D59V4, multiclass
       clus
vv      DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  T0+T1                           11                            144
  T2                               6                             72
  T3                               5                             59
  T4                               1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V5, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED    20   0
  DEL PEAK 30(20P12.1) WILD-TYPE 202   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED     20    0
  DEL PEAK 30(20P12.1) WILD-TYPE  202    3
   clus
vv  DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  0                           20                            202
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 30(20P12.1) MUTATED    20   1   2
  DEL PEAK 30(20P12.1) WILD-TYPE 218   3  67
D59V6, multiclass
    clus
vv   DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  M0                           20                            218
  M1                            1                              3
  MX                            2                             67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED     8  15
  DEL PEAK 30(20P12.1) WILD-TYPE  92 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      8   15
  DEL PEAK 30(20P12.1) WILD-TYPE   92  196
        clus
vv       DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  FEMALE                            8                             92
  MALE                             15                            196
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 30(20P12.1) MUTATED                         1
  DEL PEAK 30(20P12.1) WILD-TYPE                       1
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 30(20P12.1) MUTATED                         21
  DEL PEAK 30(20P12.1) WILD-TYPE                      282
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 30(20P12.1) MUTATED                                  1
  DEL PEAK 30(20P12.1) WILD-TYPE                                5
D59V8, multiclass
                                  clus
vv                                 DEL PEAK 30(20P12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     1
  HEPATOCELLULAR CARCINOMA                                   21
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 30(20P12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       1
  HEPATOCELLULAR CARCINOMA                                    282
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              5
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(20P12.1) MUTATED    22   0   0   1
  DEL PEAK 30(20P12.1) WILD-TYPE 252  14   1  15
D59V9, multiclass
    clus
vv   DEL PEAK 30(20P12.1) MUTATED DEL PEAK 30(20P12.1) WILD-TYPE
  R0                           22                            252
  R1                            0                             14
  R2                            0                              1
  RX                            1                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(20P12.1) MUTATED                                  0    14
  DEL PEAK 30(20P12.1) WILD-TYPE                                1   127
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(20P12.1) MUTATED                           0     9
  DEL PEAK 30(20P12.1) WILD-TYPE                        15   136
D59V10, multiclass
                                  clus
vv                                 DEL PEAK 30(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      14
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       9
                                  clus
vv                                 DEL PEAK 30(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       127
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       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"
D59V11, binary
                                cls
clus                               0   1
  DEL PEAK 30(20P12.1) MUTATED     1  21
  DEL PEAK 30(20P12.1) WILD-TYPE   7 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(20P12.1) MUTATED      1   21
  DEL PEAK 30(20P12.1) WILD-TYPE    7  266
                        clus
vv                       DEL PEAK 30(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           21
                        clus
vv                       DEL PEAK 30(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            266
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 31(22Q12.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(22Q12.1) MUTATED    39  20
  DEL PEAK 31(22Q12.1) WILD-TYPE 161  72
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            59                            233 
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                            20                             72 
$`DEL PEAK 31(22Q12.1) MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 
       10.78        37.32        27.52        13.84         0.26         9.50 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-A1HT TCGA-DD-A113 
       14.60         7.46        13.45         2.86         3.32        79.73 
TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A4 
       37.78         2.60        66.31        55.69         5.62        20.12 
TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP 
      107.11        32.52        26.83        30.51        73.81       108.76 
TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADF TCGA-DD-AADJ 
        9.30         0.53         5.62        34.09         3.78        24.00 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAVR TCGA-ED-A459 
        5.29         7.10         9.86        16.37        72.26        13.41 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-FV-A495 
        0.23         0.20         0.20        13.15        10.98         0.03 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAV3 
       60.36         1.22        51.06        14.70         1.84         9.17 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO 
       17.06        11.84        13.38        18.38        20.71        10.85 
TCGA-QA-A7B7 TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-AB4B TCGA-ZS-A9CF 
        2.04        24.13        14.40         4.01        74.24 

$`DEL PEAK 31(22Q12.1) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69I TCGA-BD-A3ER 
       69.57         5.03        44.42        22.36        12.72         4.80 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 
        0.66         0.07         0.39         3.39         4.24         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10         0.13        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z 
        6.02        29.16        18.35        13.64        21.14        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 
       25.81         7.66        70.06        17.59       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        33.14        73.38        30.97        30.15 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        10.98         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      100.96        13.48        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        40.77        38.04         5.59         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        33.83        22.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       13.97        28.41        25.08        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW 
       17.33         3.02         3.95        57.27         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.67         9.86         9.63         9.47         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS 
       15.65        15.65        35.08        79.07        79.10        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       61.87        61.38        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        47.70        12.69        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.41         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        32.45        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U 
        8.12         6.38         0.13         0.33         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
       25.64         5.92        19.53        19.23        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10         7.76        12.03         5.98        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
       11.80         9.70         0.89         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.20         2.66        37.71        20.75         4.01         2.14 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75H TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 
       12.85        58.88        16.37         4.44        21.01        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
       19.04        15.39        15.52        14.96        17.29         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04         8.32         4.57         1.02         0.99 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55         4.67        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       24.43        12.99        45.57        35.05         8.22 

  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                        108.76                         113.00 
  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE 
                         13.41                          15.39 
[1] "0.0 - 108.8 (13.4)" "0.1 - 113.0 (15.4)"
[1] "hr=" "1.1"
D60V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 31(22Q12.1) MUTATED        26       22         0         11
  DEL PEAK 31(22Q12.1) WILD-TYPE     120       50         2         41
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 31(22Q12.1) MUTATED            1          2        1         0
  DEL PEAK 31(22Q12.1) WILD-TYPE          6          5        1         1
                                vv
clus                             STAGE IVB
  DEL PEAK 31(22Q12.1) MUTATED           0
  DEL PEAK 31(22Q12.1) WILD-TYPE         2
D60V3, multiclass
            clus
vv           DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  STAGE I                              26                            120
  STAGE II                             22                             50
  STAGE III                             0                              2
  STAGE IIIA                           11                             41
  STAGE IIIB                            1                              6
  STAGE IIIC                            2                              5
  STAGE IV                              1                              1
  STAGE IVA                             0                              1
  STAGE IVB                             0                              2
[1] 9 2
[1] 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(22Q12.1) MUTATED      26  25  12   3
  DEL PEAK 31(22Q12.1) WILD-TYPE   129  53  52   9
D60V4, multiclass
       clus
vv      DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  T0+T1                           26                            129
  T2                              25                             53
  T3                              12                             52
  T4                               3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V5, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q12.1) MUTATED    44   0
  DEL PEAK 31(22Q12.1) WILD-TYPE 178   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED     44    0
  DEL PEAK 31(22Q12.1) WILD-TYPE  178    3
   clus
vv  DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  0                           44                            178
  1                            0                              3
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 31(22Q12.1) MUTATED    53   1  12
  DEL PEAK 31(22Q12.1) WILD-TYPE 185   3  57
D60V6, multiclass
    clus
vv   DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  M0                           53                            185
  M1                            1                              3
  MX                           12                             57
[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"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q12.1) MUTATED    26  40
  DEL PEAK 31(22Q12.1) WILD-TYPE  74 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED     26   40
  DEL PEAK 31(22Q12.1) WILD-TYPE   74  171
        clus
vv       DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  FEMALE                           26                             74
  MALE                             40                            171
[1] 2 2
[1] FALSE
                                vv
clus                             FIBROLAMELLAR CARCINOMA
  DEL PEAK 31(22Q12.1) MUTATED                         2
  DEL PEAK 31(22Q12.1) WILD-TYPE                       0
                                vv
clus                             HEPATOCELLULAR CARCINOMA
  DEL PEAK 31(22Q12.1) MUTATED                         63
  DEL PEAK 31(22Q12.1) WILD-TYPE                      240
                                vv
clus                             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 31(22Q12.1) MUTATED                                  1
  DEL PEAK 31(22Q12.1) WILD-TYPE                                5
D60V8, multiclass
                                  clus
vv                                 DEL PEAK 31(22Q12.1) MUTATED
  FIBROLAMELLAR CARCINOMA                                     2
  HEPATOCELLULAR CARCINOMA                                   63
  HEPATOCHOLANGIOCARCINOMA (MIXED)                            1
                                  clus
vv                                 DEL PEAK 31(22Q12.1) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                       0
  HEPATOCELLULAR CARCINOMA                                    240
  HEPATOCHOLANGIOCARCINOMA (MIXED)                              5
[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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(22Q12.1) MUTATED    54   5   0   6
  DEL PEAK 31(22Q12.1) WILD-TYPE 220   9   1  10
D60V9, multiclass
    clus
vv   DEL PEAK 31(22Q12.1) MUTATED DEL PEAK 31(22Q12.1) WILD-TYPE
  R0                           54                            220
  R1                            5                              9
  R2                            0                              1
  RX                            6                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(22Q12.1) MUTATED                                  0    24
  DEL PEAK 31(22Q12.1) WILD-TYPE                                1   117
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(22Q12.1) MUTATED                           7    34
  DEL PEAK 31(22Q12.1) WILD-TYPE                         8   111
D60V10, multiclass
                                  clus
vv                                 DEL PEAK 31(22Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      24
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 31(22Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                       117
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                       111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                                cls
clus                               0   1
  DEL PEAK 31(22Q12.1) MUTATED     2  58
  DEL PEAK 31(22Q12.1) WILD-TYPE   6 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(22Q12.1) MUTATED      2   58
  DEL PEAK 31(22Q12.1) WILD-TYPE    6  229
                        clus
vv                       DEL PEAK 31(22Q12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           58
                        clus
vv                       DEL PEAK 31(22Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            229
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 32(22Q13.32) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(22Q13.32) MUTATED    38  26
  DEL PEAK 32(22Q13.32) WILD-TYPE 162  66
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             64                             228 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                             26                              66 
$`DEL PEAK 32(22Q13.32) MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KF 
       10.78        37.32        27.52        23.34        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-A1HT 
       22.36         9.50         7.46        13.45         2.86         3.32 
TCGA-CC-A3M9 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A1EB TCGA-DD-A39X 
        0.10        79.73        37.78        83.57        66.31        55.69 
TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB 
        5.62       102.74       107.11        13.78        33.14        32.52 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-AAC8 
       26.83        30.51        73.81       108.76         9.30         0.53 
TCGA-DD-AACZ TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE3 
        5.62        28.41         3.78         5.29         7.10         9.86 
TCGA-DD-AAEE TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP 
       16.37        13.41         0.23         0.20         0.20        13.15 
TCGA-EP-A2KB TCGA-FV-A2QR TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A3CJ 
       10.98        19.10        60.36         1.22        51.06        19.53 
TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAV3 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 
       14.70         1.84         9.17        17.06        11.84        13.38 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 
       18.38        20.71        10.85        58.88        21.01         2.04 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-AB4B TCGA-ZS-A9CF 
       24.13        14.40         4.01        74.24 

$`DEL PEAK 32(22Q13.32) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 
       46.78        27.52         2.99        25.32         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-BW-A5NO 
        5.03        44.42        14.60        12.72         4.80         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.07         0.39         3.39         4.24         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        0.13        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        90.71        79.40        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        13.64        21.14        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND 
       70.06        17.59        20.12         0.36        30.61        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ 
       30.97        30.15        39.78        56.25        29.56        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        10.98         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        27.72       100.96        13.48        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       59.18        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        60.10         0.30         1.91        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       13.15        14.33        48.49        40.77        38.04         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ 
       31.53        30.58        29.26        13.97        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       24.13        20.91         0.39        17.33         3.02         3.95 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       57.27         8.28         6.67         9.67         9.86         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.47         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       14.79        12.16        15.45        15.65        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        79.10        72.26        59.93        61.87        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        23.97        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.33         0.39        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       19.23        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 
        5.98        11.24         8.55        11.80         9.70         0.89 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       20.75         4.01         2.14        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-NI-A8LF TCGA-O8-A75V 
        4.27         9.57        16.67        12.85        16.37         4.44 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        19.04        15.39        15.52        14.96        17.29 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04         8.32         4.57         1.02 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        0.99        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
        0.69        24.43        12.99        45.57        35.05         8.22 

  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                         108.76                          113.00 
  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE 
                         14.120                          14.695 
[1] "0.1 - 108.8 (14.1)" "0.0 - 113.0 (14.7)"
[1] "hr=" "1.2"
D61V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 32(22Q13.32) MUTATED        24       21         1         13
  DEL PEAK 32(22Q13.32) WILD-TYPE     122       51         1         39
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 32(22Q13.32) MUTATED            3          3        1         0
  DEL PEAK 32(22Q13.32) WILD-TYPE          4          4        1         1
                                 vv
clus                              STAGE IVB
  DEL PEAK 32(22Q13.32) MUTATED           0
  DEL PEAK 32(22Q13.32) WILD-TYPE         2
D61V3, multiclass
            clus
vv           DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  STAGE I                               24                             122
  STAGE II                              21                              51
  STAGE III                              1                               1
  STAGE IIIA                            13                              39
  STAGE IIIB                             3                               4
  STAGE IIIC                             3                               4
  STAGE IV                               1                               1
  STAGE IVA                              0                               1
  STAGE IVB                              0                               2
[1] 9 2
[1] 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(22Q13.32) MUTATED      24  25  16   5
  DEL PEAK 32(22Q13.32) WILD-TYPE   131  53  48   7
D61V4, multiclass
       clus
vv      DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  T0+T1                            24                             131
  T2                               25                              53
  T3                               16                              48
  T4                                5                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V5, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    47   1
  DEL PEAK 32(22Q13.32) WILD-TYPE 175   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     47    1
  DEL PEAK 32(22Q13.32) WILD-TYPE  175    2
   clus
vv  DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  0                            47                             175
  1                             1                               2
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 32(22Q13.32) MUTATED    55   1  14
  DEL PEAK 32(22Q13.32) WILD-TYPE 183   3  55
D61V6, multiclass
    clus
vv   DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  M0                            55                             183
  M1                             1                               3
  MX                            14                              55
[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"
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED    27  43
  DEL PEAK 32(22Q13.32) WILD-TYPE  73 168
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED     27   43
  DEL PEAK 32(22Q13.32) WILD-TYPE   73  168
        clus
vv       DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  FEMALE                            27                              73
  MALE                              43                             168
[1] 2 2
[1] FALSE
                                 vv
clus                              FIBROLAMELLAR CARCINOMA
  DEL PEAK 32(22Q13.32) MUTATED                         2
  DEL PEAK 32(22Q13.32) WILD-TYPE                       0
                                 vv
clus                              HEPATOCELLULAR CARCINOMA
  DEL PEAK 32(22Q13.32) MUTATED                         67
  DEL PEAK 32(22Q13.32) WILD-TYPE                      236
                                 vv
clus                              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 32(22Q13.32) MUTATED                                  1
  DEL PEAK 32(22Q13.32) WILD-TYPE                                5
D61V8, multiclass
                                  clus
vv                                 DEL PEAK 32(22Q13.32) MUTATED
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                    67
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             1
                                  clus
vv                                 DEL PEAK 32(22Q13.32) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                        0
  HEPATOCELLULAR CARCINOMA                                     236
  HEPATOCHOLANGIOCARCINOMA (MIXED)                               5
[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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(22Q13.32) MUTATED    56   5   0   7
  DEL PEAK 32(22Q13.32) WILD-TYPE 218   9   1   9
D61V9, multiclass
    clus
vv   DEL PEAK 32(22Q13.32) MUTATED DEL PEAK 32(22Q13.32) WILD-TYPE
  R0                            56                             218
  R1                             5                               9
  R2                             0                               1
  RX                             7                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(22Q13.32) MUTATED                                  1    22
  DEL PEAK 32(22Q13.32) WILD-TYPE                                0   119
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(22Q13.32) MUTATED                           6    39
  DEL PEAK 32(22Q13.32) WILD-TYPE                         9   106
D61V10, multiclass
                                  clus
vv                                 DEL PEAK 32(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       22
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       39
                                  clus
vv                                 DEL PEAK 32(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                        119
  BLACK OR AFRICAN AMERICAN                                      9
  WHITE                                                        106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, binary
                                 cls
clus                                0   1
  DEL PEAK 32(22Q13.32) MUTATED     2  60
  DEL PEAK 32(22Q13.32) WILD-TYPE   6 227
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(22Q13.32) MUTATED      2   60
  DEL PEAK 32(22Q13.32) WILD-TYPE    6  227
                        clus
vv                       DEL PEAK 32(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            60
                        clus
vv                       DEL PEAK 32(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             227
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 33(XQ26.2) MUTATION ANALYSIS
D62V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 33(XQ26.2) MUTATED    36  15
  DEL PEAK 33(XQ26.2) WILD-TYPE 164  77
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           51                           241 
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                           15                            77 
$`DEL PEAK 33(XQ26.2) MUTATED`
TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A10Z TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
        0.66        10.13         1.12         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-A3MA TCGA-CC-A3MB 
       22.36         9.50         0.07         2.86         0.07         0.10 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA TCGA-DD-A4NO TCGA-DD-A73B 
       83.57        53.33         0.46        33.14        73.81         9.30 
TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD5 TCGA-DD-AAD8 
      100.96        15.42        40.77        38.04        34.09        31.53 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADY 
       29.26        13.97        20.91         3.02         3.95         9.67 
TCGA-DD-AAE2 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7PX 
        9.47        15.45        16.37        61.87        13.41         0.20 
TCGA-ED-A7PZ TCGA-ED-A97K TCGA-FV-A3I0 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 
        0.20         0.20        27.88         0.89         2.14         1.02 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-QA-A7B7 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MC 
       13.38         5.92         2.04        15.39        15.52        14.40 
TCGA-UB-A7MF TCGA-ZP-A9D2 TCGA-ZS-A9CF 
        7.04        24.43        74.24 

$`DEL PEAK 33(XQ26.2) WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59        48.99        27.91        37.32 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       69.57        44.42        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.80         0.66         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.13        79.73        37.78       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        10.98         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       27.72        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        63.48        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       48.49         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       33.83        22.09        30.58        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR 
       24.00        24.13         0.39        17.33         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 
        7.10         8.28         6.67         9.86         9.63         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
        8.52         4.64        12.56        11.31        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       12.16        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.26        59.93        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       54.05        49.48        47.70        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.23         0.20         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV7 
       11.24         8.55        11.80         9.70         9.17         3.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        11.84        24.36        12.72         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 
       16.37         4.44        21.01        21.04        19.04        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
       14.96        17.29         1.71        15.98         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        1.02         0.99         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.21        23.57         0.69        12.99        45.57        35.05 
TCGA-ZS-A9CG 
        8.22 

  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                       100.96                        113.00 
  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE 
                        13.38                         14.96 
[1] "0.1 - 101.0 (13.4)" "0.0 - 113.0 (15.0)"
[1] "hr=" "1.1"
D62V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IIIA
  DEL PEAK 33(XQ26.2) MUTATED        23       16         0         13
  DEL PEAK 33(XQ26.2) WILD-TYPE     123       56         2         39
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 33(XQ26.2) MUTATED            0          2        0         0
  DEL PEAK 33(XQ26.2) WILD-TYPE          7          5        2         1
                               vv
clus                            STAGE IVB
  DEL PEAK 33(XQ26.2) MUTATED           0
  DEL PEAK 33(XQ26.2) WILD-TYPE         2
D62V3, multiclass
            clus
vv           DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  STAGE I                             23                           123
  STAGE II                            16                            56
  STAGE III                            0                             2
  STAGE IIIA                          13                            39
  STAGE IIIB                           0                             7
  STAGE IIIC                           2                             5
  STAGE IV                             0                             2
  STAGE IVA                            0                             1
  STAGE IVB                            0                             2
[1] 9 2
[1] 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(XQ26.2) MUTATED      23  18  15   1
  DEL PEAK 33(XQ26.2) WILD-TYPE   132  60  49  11
D62V4, multiclass
       clus
vv      DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  T0+T1                          23                           132
  T2                             18                            60
  T3                             15                            49
  T4                              1                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V5, binary
                               cls
clus                              0   1
  DEL PEAK 33(XQ26.2) MUTATED    41   1
  DEL PEAK 33(XQ26.2) WILD-TYPE 181   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED     41    1
  DEL PEAK 33(XQ26.2) WILD-TYPE  181    2
   clus
vv  DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  0                          41                           181
  1                           1                             2
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK 33(XQ26.2) MUTATED    47   0  10
  DEL PEAK 33(XQ26.2) WILD-TYPE 191   4  59
D62V6, multiclass
    clus
vv   DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  M0                          47                           191
  M1                           0                             4
  MX                          10                            59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                               cls
clus                              0   1
  DEL PEAK 33(XQ26.2) MUTATED    18  39
  DEL PEAK 33(XQ26.2) WILD-TYPE  82 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED     18   39
  DEL PEAK 33(XQ26.2) WILD-TYPE   82  172
        clus
vv       DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  FEMALE                          18                            82
  MALE                            39                           172
[1] 2 2
[1] FALSE
                               vv
clus                            FIBROLAMELLAR CARCINOMA
  DEL PEAK 33(XQ26.2) MUTATED                         0
  DEL PEAK 33(XQ26.2) WILD-TYPE                       2
                               vv
clus                            HEPATOCELLULAR CARCINOMA
  DEL PEAK 33(XQ26.2) MUTATED                         54
  DEL PEAK 33(XQ26.2) WILD-TYPE                      249
                               vv
clus                            HEPATOCHOLANGIOCARCINOMA (MIXED)
  DEL PEAK 33(XQ26.2) MUTATED                                  3
  DEL PEAK 33(XQ26.2) WILD-TYPE                                3
D62V8, multiclass
                                  clus
vv                                 DEL PEAK 33(XQ26.2) MUTATED
  FIBROLAMELLAR CARCINOMA                                    0
  HEPATOCELLULAR CARCINOMA                                  54
  HEPATOCHOLANGIOCARCINOMA (MIXED)                           3
                                  clus
vv                                 DEL PEAK 33(XQ26.2) WILD-TYPE
  FIBROLAMELLAR CARCINOMA                                      2
  HEPATOCELLULAR CARCINOMA                                   249
  HEPATOCHOLANGIOCARCINOMA (MIXED)                             3
[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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 33(XQ26.2) MUTATED    51   1   0   5
  DEL PEAK 33(XQ26.2) WILD-TYPE 223  13   1  11
D62V9, multiclass
    clus
vv   DEL PEAK 33(XQ26.2) MUTATED DEL PEAK 33(XQ26.2) WILD-TYPE
  R0                          51                           223
  R1                           1                            13
  R2                           0                             1
  RX                           5                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(XQ26.2) MUTATED                                  0    33
  DEL PEAK 33(XQ26.2) WILD-TYPE                                1   108
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(XQ26.2) MUTATED                           1    23
  DEL PEAK 33(XQ26.2) WILD-TYPE                        14   122
D62V10, multiclass
                                  clus
vv                                 DEL PEAK 33(XQ26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     33
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     23
                                  clus
vv                                 DEL PEAK 33(XQ26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                      108
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                      122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, binary
                               cls
clus                              0   1
  DEL PEAK 33(XQ26.2) MUTATED     1  52
  DEL PEAK 33(XQ26.2) WILD-TYPE   7 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 33(XQ26.2) MUTATED      1   52
  DEL PEAK 33(XQ26.2) WILD-TYPE    7  235
                        clus
vv                       DEL PEAK 33(XQ26.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       DEL PEAK 33(XQ26.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           235
[1] 2 2
[1] FALSE
